From 97174ea045326462053a743e70bffd41150203eb Mon Sep 17 00:00:00 2001
From: agdamsbo <43278243+agdamsbo@users.noreply.github.com>
Date: Wed, 27 Nov 2024 09:20:50 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20agdamsbo?=
 =?UTF-8?q?/REDCapCAST@d8ca1d9eb18e4bd01f4db4185a2cf94ee26d8b2f=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 news/index.html | 3 ++-
 pkgdown.yml     | 2 +-
 search.json     | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/news/index.html b/news/index.html
index 1aef1fe..c0d4507 100644
--- a/news/index.html
+++ b/news/index.html
@@ -39,7 +39,8 @@
 
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="24.11.4" id="redcapcast-24114">REDCapCAST 24.11.4<a class="anchor" aria-label="anchor" href="#redcapcast-24114"></a></h2>
-<p>The hosting on shinyapps.io has given a lot of trouble recently. Modyfied package structure a little around the <code><a href="../reference/shiny_cast.html">shiny_cast()</a></code>, to accommodate an alternative hosting approach with all package functions included in a script instead of requiring the package.</p>
+<p>This release attempts to solve problems hosting the shiny_cast app, while also implementing functions to preserve as much meta data as possible from the REDCap database when exporting data.</p>
+<p>The hosting on shinyapps.io has given a lot of trouble recently. Modified package structure a little around the <code><a href="../reference/shiny_cast.html">shiny_cast()</a></code>, to accommodate an alternative hosting approach with all package functions included in a script instead of requiring the package.</p>
 <ul><li><p>NEW: A new option to <code>raw_or_label</code> in <code>read_readcap_tables()</code> has been added: “both”. Get raw values with REDCap labels applied as labels. Use <code><a href="../reference/as_factor.html">as_factor()</a></code> to format factors with original labels and use the <code>gtsummary</code> package to easily get beautiful tables with original labels from REDCap. Use <code><a href="../reference/fct_drop.html">fct_drop()</a></code> to drop empty levels.</p></li>
 <li><p>NEW: fct_drop() has been added with an extension to <code><a href="https://forcats.tidyverse.org/reference/fct_drop.html" class="external-link">forcats::fct_drop()</a></code>, that works across data.frames. Use as <code><a href="../reference/fct_drop.html">fct_drop()</a></code>.</p></li>
 <li><p>CHANGE: the default data export method of <code><a href="../reference/easy_redcap.html">easy_redcap()</a></code> has been changed to use the new labelled data export with <code>read_readcap_tables()</code>.</p></li>
diff --git a/pkgdown.yml b/pkgdown.yml
index 8bb5d3b..c2be664 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   Database-creation: Database-creation.html
   REDCapCAST: REDCapCAST.html
   Shiny-app: Shiny-app.html
-last_built: 2024-11-27T09:06Z
+last_built: 2024-11-27T09:20Z
 urls:
   reference: https://agdamsbo.github.io/REDCapCAST/reference
   article: https://agdamsbo.github.io/REDCapCAST/articles
diff --git a/search.json b/search.json
index c72d25e..c20f0db 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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Mere interaction user computer network, transfer copy, conveying. interactive user interface displays “Appropriate Legal Notices” extent includes convenient prominently visible feature (1) displays appropriate copyright notice, (2) tells user warranty work (except extent warranties provided), licensees may convey work License, view copy License. interface presents list user commands options, menu, prominent item list meets criterion.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_1-source-code","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"1. 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However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions","title":"GNU General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. 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Regardless server hosts Corresponding Source, remain obligated ensure available long needed satisfy requirements. e) Convey object code using peer--peer transmission, provided inform peers object code Corresponding Source work offered general public charge subsection 6d. separable portion object code, whose source code excluded Corresponding Source System Library, need included conveying object code work. “User Product” either (1) “consumer product”, means tangible personal property normally used personal, family, household purposes, (2) anything designed sold incorporation dwelling. determining whether product consumer product, doubtful cases shall resolved favor coverage. particular product received particular user, “normally used” refers typical common use class product, regardless status particular user way particular user actually uses, expects expected use, product. product consumer product regardless whether product substantial commercial, industrial non-consumer uses, unless uses represent significant mode use product. “Installation Information” User Product means methods, procedures, authorization keys, information required install execute modified versions covered work User Product modified version Corresponding Source. information must suffice ensure continued functioning modified object code case prevented interfered solely modification made. convey object code work section , , specifically use , User Product, conveying occurs part transaction right possession use User Product transferred recipient perpetuity fixed term (regardless transaction characterized), Corresponding Source conveyed section must accompanied Installation Information. requirement apply neither third party retains ability install modified object code User Product (example, work installed ROM). requirement provide Installation Information include requirement continue provide support service, warranty, updates work modified installed recipient, User Product modified installed. 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Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. Notwithstanding provision License, material add covered work, may (authorized copyright holders material) supplement terms License terms: ) Disclaiming warranty limiting liability differently terms sections 15 16 License; b) Requiring preservation specified reasonable legal notices author attributions material Appropriate Legal Notices displayed works containing ; c) Prohibiting misrepresentation origin material, requiring modified versions material marked reasonable ways different original version; d) Limiting use publicity purposes names licensors authors material; e) Declining grant rights trademark law use trade names, trademarks, service marks; f) Requiring indemnification licensors authors material anyone conveys material (modified versions ) contractual assumptions liability recipient, liability contractual assumptions directly impose licensors authors. non-permissive additional terms considered “restrictions” within meaning section 10. Program received , part , contains notice stating governed License along term restriction, may remove term. license document contains restriction permits relicensing conveying License, may add covered work material governed terms license document, provided restriction survive relicensing conveying. add terms covered work accord section, must place, relevant source files, statement additional terms apply files, notice indicating find applicable terms. Additional terms, permissive non-permissive, may stated form separately written license, stated exceptions; requirements apply either way.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_8-termination","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"8. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"two-different-ways-to-create-a-data-base","dir":"Articles","previous_headings":"","what":"Two different ways to create a data base","title":"Database-creation","text":"REDCapCAST provides two approaches creating data dictionary aimed helping two different cases: Easily create REDCap data base existing data set. Create table Word describing variables data base use create data base. following try come suggestions use approaches.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"easy-data-set-to-data-base-workflow","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Easy data set to data base workflow","title":"Database-creation","text":"first iteration dataset data dictionary function ds2dd(), creates basic data dictionary variables stored text. sufficient just storing old datasets/spreadsheets securely REDCap. advanced ds2dd_detailed() natural development. try apply common data classes data validation assume first column id number. outputs list dataset modified variable names comply REDCap naming conventions data dictionary. dataset correctly formatted data dictionary preserve much information possible. Additional specifications DataDictionary can made manually, can uploaded modified manually graphical user interface REDCap server.","code":"d1 <- mtcars |>   dplyr::mutate(record_id = seq_len(dplyr::n())) |>   ds2dd()   d1 |>   gt::gt() d2 <- REDCapCAST::redcapcast_data |>    dplyr::mutate(record_id = seq_len(dplyr::n()),                 region=factor(region)) |>   dplyr::select(record_id, dplyr::everything()) |>   (\\(.x){     .x[!grepl(\"_complete$\",names(.x))]   })() |>    (\\(.x){     .x[!grepl(\"^redcap\",names(.x))]   })() |>     ds2dd_detailed() |>    purrr::pluck(\"meta\")   d2 |>    gt::gt()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"data-base-from-table","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Data base from table","title":"Database-creation","text":"…instructions examples coming…","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"meta-data-and-data-upload","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Meta data and data upload","title":"Database-creation","text":"Now DataDictionary can exported spreadsheet uploaded can uploaded using REDCapR package (projects “Development” status). Use one two approaches :","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"manual-upload","dir":"Articles","previous_headings":"Two different ways to create a data base > Meta data and data upload","what":"Manual upload","title":"Database-creation","text":"","code":"write.csv(dd_ls$meta, \"datadictionary.csv\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"upload-with-redcapr","dir":"Articles","previous_headings":"Two different ways to create a data base > Meta data and data upload","what":"Upload with REDCapR","title":"Database-creation","text":"“REDCap R Handbook” written interfacing REDCap R using library(keyring)store credentials chapter 1.1.","code":"REDCapR::redcap_metadata_write(   dd_ls$meta,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-4---data-upload","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Step 4 - Data upload","title":"Database-creation","text":"two options available data upload meta data upload: manual REDCapR. latter shown .","code":"REDCapR::redcap_write(   dd_ls$data,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"splitting-the-dataset","dir":"Articles","previous_headings":"","what":"Splitting the dataset","title":"REDCapCAST","text":"","code":"redcapcast_data |> gt::gt() redcapcast_meta |> gt::gt() list <-   REDCap_split(     records = redcapcast_data,     metadata = redcapcast_meta,     forms = \"all\"   ) |>    sanitize_split() str(list) #> List of 4 #>  $ baseline_data_start: tibble [6 × 14] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id                   : num [1:6] 1 2 3 4 5 6 #>   ..$ redcap_event_name           : chr [1:6] \"inclusion\" \"inclusion\" \"inclusion\" \"inclusion\" ... #>   ..$ cpr                         : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>   ..$ inclusion                   : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #>   ..$ inclusion_time              : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ... #>   .. ..- attr(*, \"units\")= chr \"secs\" #>   ..$ dob                         : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #>   ..$ age                         : num [1:6] 83 89.1 66.1 117.9 126.2 ... #>   ..$ age_integer                 : num [1:6] 83 89 66 117 126 91 #>   ..$ sex                         : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #>   ..$ cohabitation                : chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #>   ..$ hypertension                : chr [1:6] \"No\" \"No\" \"Yes\" NA ... #>   ..$ diabetes                    : chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #>   ..$ region                      : chr [1:6] \"East\" \"South\" \"North\" NA ... #>   ..$ baseline_data_start_complete: chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>   ..- attr(*, \"problems\")=<externalptr>  #>  $ mrs                : tibble [5 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id        : num [1:5] 1 2 2 3 3 #>   ..$ redcap_event_name: chr [1:5] \"inclusion\" \"inclusion\" \"follow1\" \"follow1\" ... #>   ..$ mrs_assessed     : chr [1:5] \"Yes\" \"Yes\" \"Yes\" \"Yes\" ... #>   ..$ mrs_date         : Date[1:5], format: \"2023-03-13\" \"2023-03-07\" ... #>   ..$ mrs_score        : num [1:5] 1 1 3 2 1 #>   ..$ mrs_complete     : chr [1:5] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>   ..- attr(*, \"problems\")=<externalptr>  #>  $ consensus          : tibble [0 × 5] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id         : num(0)  #>   ..$ redcap_event_name : chr(0)  #>   ..$ con_mrs           : logi(0)  #>   ..$ con_calc          : logi(0)  #>   ..$ consensus_complete: chr(0)  #>   ..- attr(*, \"problems\")=<externalptr>  #>  $ new_event          : tibble [13 × 8] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id               : num [1:13] 2 3 3 3 3 3 4 4 4 4 ... #>   ..$ redcap_event_name       : chr [1:13] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #>   ..$ redcap_repeat_instrument: chr [1:13] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #>   ..$ redcap_repeat_instance  : num [1:13] 1 1 2 1 2 3 1 2 1 2 ... #>   ..$ event_datetime          : POSIXct[1:13], format: \"2024-01-18 12:49:42\" \"2024-01-18 12:49:58\" ... #>   ..$ event_age               : num [1:13] NA NA NA NA NA NA 96 105 118 118 ... #>   ..$ event_type              : chr [1:13] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #>   ..$ new_event_complete      : chr [1:13] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>   ..- attr(*, \"problems\")=<externalptr>"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"reading-data-from-redcap","dir":"Articles","previous_headings":"","what":"Reading data from REDCap","title":"REDCapCAST","text":"function wraps demonstrated function get dataset, metadata, apply REDCap_splitfunction bit cleaning. just cuts outs steps easier approach. function works similar REDCapR::redcap_read() allowing specify fields, events forms export instead exporting whole database filtering afterwards. believe better safer, focused approach.","code":"# read_redcap_tables(uri = \"YOUR URI\", token = \"YOUR TOKEN\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"pivotting-to-wider-format","dir":"Articles","previous_headings":"","what":"Pivotting to wider format","title":"REDCapCAST","text":"","code":"redcap_wider(list) |> str() #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> 'data.frame':    6 obs. of  52 variables: #>  $ record_id                   : num  1 2 3 4 5 6 #>  $ cpr                         : chr  \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>  $ inclusion                   : Date, format: \"2023-03-13\" \"2023-03-01\" ... #>  $ inclusion_time              : 'hms' num  12:38:49 10:38:57 12:01:07 20:39:19 ... #>   ..- attr(*, \"units\")= chr \"secs\" #>  $ dob                         : Date, format: \"1940-03-12\" \"1934-02-01\" ... #>  $ age                         : num  83 89.1 66.1 117.9 126.2 ... #>  $ age_integer                 : num  83 89 66 117 126 91 #>  $ sex                         : chr  \"female\" \"male\" \"male\" \"female\" ... #>  $ cohabitation                : chr  \"Yes\" \"Yes\" \"No\" NA ... #>  $ hypertension                : chr  \"No\" \"No\" \"Yes\" NA ... #>  $ diabetes                    : chr  \"Yes\" \"No\" \"Yes\" NA ... #>  $ region                      : chr  \"East\" \"South\" \"North\" NA ... #>  $ baseline_data_start_complete: chr  \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ mrs_assessed_inclusion      : chr  \"Yes\" \"Yes\" NA NA ... #>  $ mrs_assessed_follow1        : chr  NA \"Yes\" \"Yes\" NA ... #>  $ mrs_assessed_follow2        : chr  NA NA \"Yes\" NA ... #>  $ mrs_date_inclusion          : Date, format: \"2023-03-13\" \"2023-03-07\" ... #>  $ mrs_date_follow1            : Date, format: NA \"2023-03-09\" ... #>  $ mrs_date_follow2            : Date, format: NA NA ... #>  $ mrs_score_inclusion         : num  1 1 NA NA NA NA #>  $ mrs_score_follow1           : num  NA 3 2 NA NA NA #>  $ mrs_score_follow2           : num  NA NA 1 NA NA NA #>  $ mrs_complete_inclusion      : chr  \"Incomplete\" \"Incomplete\" NA NA ... #>  $ mrs_complete_follow1        : chr  NA \"Incomplete\" \"Incomplete\" NA ... #>  $ mrs_complete_follow2        : chr  NA NA \"Incomplete\" NA ... #>  $ con_mrs                     : logi  NA NA NA NA NA NA #>  $ con_calc                    : logi  NA NA NA NA NA NA #>  $ consensus_complete          : chr  NA NA NA NA ... #>  $ event_datetime_1_follow1    : POSIXct, format: NA \"2024-01-18 12:49:42\" ... #>  $ event_datetime_1_follow2    : POSIXct, format: NA NA ... #>  $ event_age_1_follow1         : num  NA NA NA 96 127 NA #>  $ event_age_1_follow2         : num  NA NA NA 118 NA NA #>  $ event_type_1_follow1        : chr  NA \"TIA\" \"AIS\" \"TIA\" ... #>  $ event_type_1_follow2        : chr  NA NA \"ICH\" \"AIS\" ... #>  $ new_event_complete_1_follow1: chr  NA \"Incomplete\" \"Incomplete\" \"Complete\" ... #>  $ new_event_complete_1_follow2: chr  NA NA \"Incomplete\" \"Complete\" ... #>  $ event_datetime_2_follow1    : POSIXct, format: NA NA ... #>  $ event_datetime_2_follow2    : POSIXct, format: NA NA ... #>  $ event_datetime_3_follow1    : POSIXct, format: NA NA ... #>  $ event_datetime_3_follow2    : POSIXct, format: NA NA ... #>  $ event_age_2_follow1         : num  NA NA NA 105 127 NA #>  $ event_age_2_follow2         : num  NA NA NA 118 NA NA #>  $ event_age_3_follow1         : num  NA NA NA NA NA NA #>  $ event_age_3_follow2         : num  NA NA NA 118 NA NA #>  $ event_type_2_follow1        : chr  NA NA \"ICH\" \"TIA\" ... #>  $ event_type_2_follow2        : chr  NA NA \"TIA\" \"ICH\" ... #>  $ event_type_3_follow1        : chr  NA NA NA NA ... #>  $ event_type_3_follow2        : chr  NA NA \"AIS\" \"Unknown\" ... #>  $ new_event_complete_2_follow1: chr  NA NA \"Incomplete\" \"Complete\" ... #>  $ new_event_complete_2_follow2: chr  NA NA \"Incomplete\" \"Incomplete\" ... #>  $ new_event_complete_3_follow1: chr  NA NA NA NA ... #>  $ new_event_complete_3_follow2: chr  NA NA \"Incomplete\" \"Complete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer. Paul Egeler. Author.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo , Egeler P (2024). REDCapCAST: REDCap Metadata Casting Castellated Data Handling. R package version 24.11.4, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{,   title = {REDCapCAST: REDCap Metadata Casting and Castellated Data Handling},   author = {Andreas Gammelgaard Damsbo and Paul Egeler},   year = {2024},   note = {R package version 24.11.4, https://agdamsbo.github.io/REDCapCAST/},   url = {https://github.com/agdamsbo/REDCapCAST}, }"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"redcapcast-package-","dir":"","previous_headings":"","what":"REDCap Metadata Casting and Castellated Data Handling","title":"REDCap Metadata Casting and Castellated Data Handling","text":"Casting metadata REDCap database creation handling castellated data using repeated instruments longitudinal projects REDCap. implemented app-interface easy database creation accessible available run locally shiny_cast() allowing easily create REDCap database based existing spreadsheet. Export data REDCap different formats handling castellated data, default export requested data, mainly read_redcap_tables(). REDCapCAST initially build , still includes code pegeler/REDCapRITS, relies functions REDCapR-project","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"history","dir":"","previous_headings":"","what":"History","title":"REDCap Metadata Casting and Castellated Data Handling","text":"package originally forked pegeler/REDCapRITS. REDCapRITS represents great extensive work handle castellated REDCap data different programming languages. REDCapCAST evolved much just handling castellated data detatched original project still relying main REDCap_split function. access REDCap database build outstanding work REDCapR. package really started frustration PhD health science hearing colleagues complaining “castellated” data formatting REDCap exports longitudinal projects used wide data. led bad decisions building databases avoiding repeated instruments. package solves challenges, solutions also implemented else like redcapAPI REDCapTidieR packages, bigger project. help new PhD students researchers, also worked creating helper/wrapper-functions ease data access. Documentation ’s way. advanced uses, consider using redcapAPI REDCapR packages.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"REDCap Metadata Casting and Castellated Data Handling","text":"plan package bundled Handbook working REDCap R. work progress limited time available. Please feel free contact create issue ideas future additions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"installation-and-use","dir":"","previous_headings":"","what":"Installation and use","title":"REDCap Metadata Casting and Castellated Data Handling","text":"package available CRAN. Install latest version: Install latest version directly GitHub: Launch REDCapCAST app interface directly machine:","code":"install.packages(\"REDCapCAST\") require(\"remotes\") remotes::install_github(\"agdamsbo/REDCapCAST\") REDCapCAST::shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"REDCap Metadata Casting and Castellated Data Handling","text":"Please note REDCapCAST project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCapCAST-package.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","title":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","text":"Casting metadata REDCap database creation handling castellated data using repeated instruments longitudinal projects 'REDCap'. Keeps focused data export approach, allowing export required data database. Also casting new REDCap databases based datasets sources. Originally forked R part 'REDCapRITS' Paul Egeler. See https://github.com/pegeler/REDCapRITS. 'REDCap' (Research Electronic Data Capture) secure, web-based software platform designed support data capture research studies, providing 1) intuitive interface validated data capture; 2) audit trails tracking data manipulation export procedures; 3) automated export procedures seamless data downloads common statistical packages; 4) procedures data integration interoperability external sources (Harris et al (2009) doi:10.1016/j.jbi.2008.08.010 ; Harris et al (2019) doi:10.1016/j.jbi.2019.103208 ).","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCapCAST-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","text":"Maintainer: Andreas Gammelgaard Damsbo agdamsbo@clin.au.dk (ORCID) Authors: Paul Egeler paulegeler@gmail.com (ORCID)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split REDCap repeating instruments table into multiple tables — REDCap_split","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"take output REDCap export split base table child tables repeating instrument. Metadata used determine fields included resultant table.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"REDCap_split(   records,   metadata,   primary_table_name = \"\",   forms = c(\"repeating\", \"all\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"records Exported project records. May data.frame, response, character vector containing JSON API call. metadata Project metadata (data dictionary). May data.frame, response, character vector containing JSON API call. primary_table_name Name given list element primary output table (described README.md). Ignored forms = ''. forms Indicate whether create separate tables repeating instruments forms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"list \"data.frame\"s. number tables differ   depending forms option selected. 'repeating': one base table one     tables repeating instrument. '': data.frame instrument, regardless     whether repeating instrument .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"Paul W. Egeler, M.S., GStat","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"if (FALSE) { # \\dontrun{ # Using an API call -------------------------------------------------------  library(RCurl)  # Get the records records <- postForm(   uri = api_url, # Supply your site-specific URI   token = api_token, # Supply your own API token   content = \"record\",   format = \"json\",   returnFormat = \"json\" )  # Get the metadata metadata <- postForm(   uri = api_url, # Supply your site-specific URI   token = api_token, # Supply your own API token   content = \"metadata\",   format = \"json\" )  # Convert exported JSON strings into a list of data.frames REDCapRITS::REDCap_split(records, metadata)  # Using a raw data export -------------------------------------------------  # Get the records records <- read.csv(\"/path/to/data/ExampleProject_DATA_2018-06-03_1700.csv\")  # Get the metadata metadata <- read.csv(   \"/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv\" )  # Split the tables REDCapRITS::REDCap_split(records, metadata)  # In conjunction with the R export script ---------------------------------  # You must set the working directory first since the REDCap data export # script contains relative file references. old <- getwd() setwd(\"/path/to/data/\")  # Run the data export script supplied by REDCap. # This will create a data.frame of your records called 'data' source(\"ExampleProject_R_2018-06-03_1700.r\")  # Get the metadatan metadata <- read.csv(\"ExampleProject_DataDictionary_2018-06-03.csv\")  # Split the tables REDCapRITS::REDCap_split(data, metadata) setwd(old) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if vector is all NA — all_na","title":"Check if vector is all NA — all_na","text":"Check vector NA","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if vector is all NA — all_na","text":"","code":"all_na(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if vector is all NA — all_na","text":"data vector data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if vector is all NA — all_na","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if vector is all NA — all_na","text":"","code":"rep(NA, 4) |> all_na() #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"Preserve factor levels REDCap data dictionary data export","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"","code":"apply_factor_labels(data, meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"data REDCap exported data set meta REDCap data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply REDCap filed labels to data frame — apply_field_label","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"Apply REDCap filed labels data frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"","code":"apply_field_label(data, meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"data REDCap exported data set meta REDCap data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert labelled vectors to factors while preserving attributes — as_factor","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"extends [forcats::as_factor()] well [haven::as_factor()], appending original attributes except \"class\" converting factor avoid ta loss case rich formatted labelled data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"","code":"as_factor(x, ...)  # S3 method for class 'factor' as_factor(x, ...)  # S3 method for class 'logical' as_factor(x, ...)  # S3 method for class 'numeric' as_factor(x, ...)  # S3 method for class 'character' as_factor(x, ...)  # S3 method for class 'haven_labelled' as_factor(   x,   levels = c(\"default\", \"labels\", \"values\", \"both\"),   ordered = FALSE,   ... )  # S3 method for class 'labelled' as_factor(   x,   levels = c(\"default\", \"labels\", \"values\", \"both\"),   ordered = FALSE,   ... )  # S3 method for class 'redcapcast_labelled' as_factor(   x,   levels = c(\"default\", \"labels\", \"values\", \"both\"),   ordered = FALSE,   ... )  # S3 method for class 'data.frame' as_factor(x, ..., only_labelled = TRUE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"x Object coerce factor. ... arguments passed method. levels create levels generated factor: * \"default\": uses labels available, otherwise values.     Labels sorted value.   * \"\": like \"default\", pastes together level value   * \"label\": use labels; unlabelled values become `NA`   * \"values\": use values ordered `TRUE` create ordered (ordinal) factor, `FALSE` (default) create regular (nominal) factor. only_labelled apply labelled columns?","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"Please refer parent functions extended documentation. avoid redundancy calls errors, functions copy-pasted ","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"","code":"# will preserve all attributes c(1, 4, 3, \"A\", 7, 8, 1) |> as_factor() #> Warning: invalid roman numeral: A #> [1] 1 4 3 A 7 8 1 #> Levels: 1 4 3 A 7 8 structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10) ) |>   as_factor() |>   dput() #> structure(c(1L, 2L, 3L, 2L, 5L, 4L), levels = c(\"1\", \"2\", \"3\",  #> \"9\", \"10\"), class = \"factor\", labels = c(Unknown = 9, Refused = 10 #> ))  structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |>   as_factor() #> [1] 1       2       3       2       Refused Unknown #> attr(,\"labels\") #> Unknown Refused  #>       9      10  #> Levels: 1 2 3 Unknown Refused"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List-base regex case_when — case_match_regex_list","title":"List-base regex case_when — case_match_regex_list","text":"Mimics case_when list regex patterns values. Used date/time validation generation name vector. Like case_when, matches order priority. Primarily used REDCapCAST data type coding systematic variable naming.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List-base regex case_when — case_match_regex_list","text":"","code":"case_match_regex_list(data, match.list, .default = NA)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List-base regex case_when — case_match_regex_list","text":"data vector match.list list case matches .default Default value non-matches. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List-base regex case_when — case_match_regex_list","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List-base regex case_when — case_match_regex_list","text":"","code":"case_match_regex_list(   c(\"test_date\", \"test_time\", \"test_tida\", \"test_tid\"),   list(date_dmy = \"_dat[eo]$\", time_hh_mm_ss = \"_ti[md]e?$\") ) #> [1] \"date_dmy\"      \"time_hh_mm_ss\" NA              \"time_hh_mm_ss\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":null,"dir":"Reference","previous_headings":"","what":"Overview of REDCapCAST data for shiny — cast_data_overview","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"Overview REDCapCAST data shiny","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"","code":"cast_data_overview(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"data list class 'REDCapCAST'","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"gt object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":null,"dir":"Reference","previous_headings":"","what":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"Overview REDCapCAST meta data shiny","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"","code":"cast_meta_overview(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"data list class 'REDCapCAST'","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"gt object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple function to generate REDCap choices from character vector — char2choice","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"Simple function generate REDCap choices character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"","code":"char2choice(data, char.split = \"/\", raw = NULL, .default = NA)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"data vector char.split splitting character(s) raw specific values. Can used options length. .default default value missing. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"","code":"char2choice(c(\"yes/no\",\"  yep. / nope  \",\"\",NA,\"what\"),.default=NA) #> [1] \"1, yes | 2, no\"    \"1, yep. | 2, nope\" NA                  #> [4] NA                  \"1, what\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple function to generate REDCap branching logic from character vector — char2cond","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"Simple function generate REDCap branching logic character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"","code":"char2cond(   data,   minor.split = \",\",   major.split = \";\",   major.sep = \" or \",   .default = NA )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"data vector minor.split minor split major.split major split major.sep argument separation. Default \" \". .default default value missing. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"","code":"#data <- dd_inst$betingelse #c(\"Extubation_novent, 2; Pacu_delay, 1\") |> char2cond()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"simple function remove rich text formatting field label save first paragraph ('<p>...<\/p>').","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"","code":"clean_field_label(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"data field label","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"","code":"clean_field_label(\"<div class=\\\"rich-text-field-label\\\"><p>Fazekas score<\/p><\/div>\") #> [1] \"Fazekas score\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":null,"dir":"Reference","previous_headings":"","what":"clean_redcap_name — clean_redcap_name","title":"clean_redcap_name — clean_redcap_name","text":"Stepwise removal non-alphanumeric characters, trailing white space, substitutes spaces underscores converts lower case. Trying make different naming conventions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clean_redcap_name — clean_redcap_name","text":"","code":"clean_redcap_name(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clean_redcap_name — clean_redcap_name","text":"x vector data frame cleaning","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clean_redcap_name — clean_redcap_name","text":"vector data frame, format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Compacting a vector of any length with or without names — compact_vec","title":"Compacting a vector of any length with or without names — compact_vec","text":"Compacting vector length without names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compacting a vector of any length with or without names — compact_vec","text":"","code":"compact_vec(data, nm.sep = \": \", val.sep = \"; \")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compacting a vector of any length with or without names — compact_vec","text":"data vector, optionally named nm.sep string separating name value val.sep string separating values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compacting a vector of any length with or without names — compact_vec","text":"character string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compacting a vector of any length with or without names — compact_vec","text":"","code":"sample(seq_len(4), 20, TRUE) |>   as_factor() |>   named_levels() |>   sort() |>   compact_vec() #> [1] \"1: 1; 2: 2; 3: 3; 4: 4\" 1:6 |> compact_vec() #> [1] \"1; 2; 3; 4; 5; 6\" \"test\" |> compact_vec() #> [1] \"test\" sample(letters[1:9], 20, TRUE) |> compact_vec() #> [1] \"g; e; e; b; f; d; b; c; i; f; g; e; f; i; f; e; b; a; d; h\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"Create two-column HTML table data piping REDCap instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"","code":"create_html_table(text, variable)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"text descriptive text variable variable pipe","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"","code":"create_html_table(text = \"Patient ID\", variable = c(\"[cpr]\")) #> <table style=\"border-collapse: collapse; width: 100%;\" border=\"0\"> <tbody><tr> <td style=\"width: 58%;\"> <h5><span style=\"font-weight: normal;\">Patient ID<br /><\/span><\/h5> <\/td> <td style=\"width: 42%; text-align: left;\"> <h5><span style=\"font-weight: bold;\">[cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> create_html_table(text = paste(\"assessor\", 1:2, sep = \"_\"), variable = c(\"[cpr]\")) #> <table style=\"border-collapse: collapse; width: 100%;\" border=\"0\"> <tbody><tr> <td style=\"width: 58%;\"> <h5><span style=\"font-weight: normal;\">assessor_1<br /><\/span><\/h5> <\/td> <td style=\"width: 42%; text-align: left;\"> <h5><span style=\"font-weight: bold;\">[cpr]<\/span><\/h5> <\/td> <\/tr><tr> <td style=\"width: 58%;\"> <h5><span style=\"font-weight: normal;\">assessor_2<br /><\/span><\/h5> <\/td> <td style=\"width: 42%; text-align: left;\"> <h5><span style=\"font-weight: bold;\">[cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> # create_html_table(text = c(\"CPR nummer\",\"Word\"), variable = c(\"[cpr][1]\", \"[cpr][2]\", \"[test]\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"Metadata can added editing data dictionary project initial design phase. want later add new instruments, function can used create () instrument(s) add project production.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"","code":"create_instrument_meta(data, dir = here::here(\"\"), record.id = TRUE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"data metadata relevant instrument. `ds2dd_detailed()` dir destination dir instrument zip. Default current WD. record.id flag omit first row data dictionary assuming record_id field included instrument. Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"","code":"if (FALSE) { # \\dontrun{ data <- iris |>   ds2dd_detailed(     add.auto.id = TRUE,     form.name = sample(c(\"b\", \"c\"),       size = 6,       replace = TRUE, prob = rep(.5, 2)     )   ) |>   purrr::pluck(\"meta\") # data |> create_instrument_meta()  data <- iris |>   ds2dd_detailed(add.auto.id = FALSE) |>   purrr::pluck(\"data\") iris |>   setNames(glue::glue(\"{sample(x = c('a','b'),size = length(ncol(iris)), replace=TRUE,prob = rep(x=.5,2))}__{names(iris)}\")) |>   ds2dd_detailed(form.sep = \"__\") data |>   purrr::pluck(\"meta\") |>   create_instrument_meta(record.id = FALSE) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert single digits to words — d2w","title":"Convert single digits to words — d2w","text":"Convert single digits words","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert single digits to words — d2w","text":"","code":"d2w(x, lang = \"en\", neutrum = FALSE, everything = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert single digits to words — d2w","text":"x data. Handle vectors, data.frames lists lang language. Danish (da) English (en), Default \"en\" neutrum numbers depending counted word everything flag also split numbers >9 single digits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert single digits to words — d2w","text":"returns characters format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert single digits to words — d2w","text":"","code":"d2w(c(2:8, 21)) #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" \"21\"    d2w(data.frame(2:7, 3:8, 1), lang = \"da\", neutrum = TRUE) #>   X2.7 X3.8 X1 #> 1   to  tre et #> 2  tre fire et #> 3 fire  fem et #> 4  fem seks et #> 5 seks  syv et #> 6  syv otte et  ## If everything=T, also larger numbers are reduced. ## Elements in the list are same length as input d2w(list(2:8, c(2, 6, 4, 23), 2), everything = TRUE) #> [[1]] #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" #>  #> [[2]] #> [1] \"two\"       \"six\"       \"four\"      \"two three\" #>  #> [[3]] #> [1] \"two\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"Works well `project.aid::docx2list()`. Allows defining database text document (see provided template) easier use data base creation. approach allows easier collaboration defining database. generic case data frame variable names values column. format like REDCap data dictionary, gives options formatting.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"","code":"doc2dd(   data,   instrument.name,   col.variables = 1,   list.datetime.format = list(date_dmy = \"_dat[eo]$\", time_hh_mm_ss = \"_ti[md]e?$\"),   col.description = NULL,   col.condition = NULL,   col.subheader = NULL,   subheader.tag = \"h2\",   condition.minor.sep = \",\",   condition.major.sep = \";\",   col.calculation = NULL,   col.choices = NULL,   choices.char.sep = \"/\",   missing.default = NA )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"data tibble data.frame variable names one column instrument.name character vector length one. Instrument name. col.variables variable names column (default = 1), allows dplyr subsetting list.datetime.format formatting date/time detection. See `case_match_regex_list()` col.description descriptions column, allows dplyr subsetting. empty, variable names used. col.condition conditions branching column, allows dplyr subsetting. See `char2cond()`. col.subheader sub-header column, allows dplyr subsetting. See `format_subheader()`. subheader.tag formatting tag. Default \"h2\" condition.minor.sep condition split minor. See `char2cond()`. Default \",\". condition.major.sep condition split major. See `char2cond()`. Default \";\". col.calculation calculations column. written exact. Character vector. col.choices choices column. See `char2choice()`. choices.char.sep choices split. See `char2choice()`. Default \"/\". missing.default value missing fields. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"tibble data.frame (data)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"","code":"# data <- dd_inst # data |> doc2dd(instrument.name = \"evt\", # col.description = 3, # col.condition = 4, # col.subheader = 2, # col.calculation = 5, # col.choices = 6)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"(DEPRECATED) Data set to data dictionary function — ds2dd","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Creates basic data dictionary skeleton. Please see `ds2dd_detailed()` advanced function.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"ds2dd(   ds,   record.id = \"record_id\",   form.name = \"basis\",   field.type = \"text\",   field.label = NULL,   include.column.names = FALSE,   metadata = names(REDCapCAST::redcapcast_meta) )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"ds data set record.id name column number id variable, moved first row data dictionary, character integer. Default \"record_id\". form.name vector form names, character string, length 1 length equal number variables. Default \"basis\". field.type vector field types, character string, length 1 length equal number variables. Default \"text. field.label vector form names, character string, length 1 length equal number variables. Default NULL identical field names. include.column.names Flag give detailed output including new column names original data set upload. metadata Metadata column names. Default included names(REDCapCAST::redcapcast_meta).","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"data.frame list data.frame vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Migrated stRoke ds2dd(). Fits better functionality 'REDCapCAST'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"redcapcast_data$record_id <- seq_len(nrow(redcapcast_data)) ds2dd(redcapcast_data, include.column.names=TRUE) #> $DataDictionary #>                      field_name form_name section_header field_type #> 1                     record_id     basis             NA       text #> 2             redcap_event_name     basis             NA       text #> 3      redcap_repeat_instrument     basis             NA       text #> 4        redcap_repeat_instance     basis             NA       text #> 5                           cpr     basis             NA       text #> 6                     inclusion     basis             NA       text #> 7                inclusion_time     basis             NA       text #> 8                           dob     basis             NA       text #> 9                           age     basis             NA       text #> 10                  age_integer     basis             NA       text #> 11                          sex     basis             NA       text #> 12                 cohabitation     basis             NA       text #> 13                 hypertension     basis             NA       text #> 14                     diabetes     basis             NA       text #> 15                       region     basis             NA       text #> 16 baseline_data_start_complete     basis             NA       text #> 17                 mrs_assessed     basis             NA       text #> 18                     mrs_date     basis             NA       text #> 19                    mrs_score     basis             NA       text #> 20                 mrs_complete     basis             NA       text #> 21                      con_mrs     basis             NA       text #> 22                     con_calc     basis             NA       text #> 23           consensus_complete     basis             NA       text #> 24               event_datetime     basis             NA       text #> 25                    event_age     basis             NA       text #> 26                   event_type     basis             NA       text #> 27           new_event_complete     basis             NA       text #>                     field_label select_choices_or_calculations field_note #> 1                     record_id                             NA         NA #> 2             redcap_event_name                             NA         NA #> 3      redcap_repeat_instrument                             NA         NA #> 4        redcap_repeat_instance                             NA         NA #> 5                           cpr                             NA         NA #> 6                     inclusion                             NA         NA #> 7                inclusion_time                             NA         NA #> 8                           dob                             NA         NA #> 9                           age                             NA         NA #> 10                  age_integer                             NA         NA #> 11                          sex                             NA         NA #> 12                 cohabitation                             NA         NA #> 13                 hypertension                             NA         NA #> 14                     diabetes                             NA         NA #> 15                       region                             NA         NA #> 16 baseline_data_start_complete                             NA         NA #> 17                 mrs_assessed                             NA         NA #> 18                     mrs_date                             NA         NA #> 19                    mrs_score                             NA         NA #> 20                 mrs_complete                             NA         NA #> 21                      con_mrs                             NA         NA #> 22                     con_calc                             NA         NA #> 23           consensus_complete                             NA         NA #> 24               event_datetime                             NA         NA #> 25                    event_age                             NA         NA #> 26                   event_type                             NA         NA #> 27           new_event_complete                             NA         NA #>    text_validation_type_or_show_slider_number text_validation_min #> 1                                          NA                  NA #> 2                                          NA                  NA #> 3                                          NA                  NA #> 4                                          NA                  NA #> 5                                          NA                  NA #> 6                                          NA                  NA #> 7                                          NA                  NA #> 8                                          NA                  NA #> 9                                          NA                  NA #> 10                                         NA                  NA #> 11                                         NA                  NA #> 12                                         NA                  NA #> 13                                         NA                  NA #> 14                                         NA                  NA #> 15                                         NA                  NA #> 16                                         NA                  NA #> 17                                         NA                  NA #> 18                                         NA                  NA #> 19                                         NA                  NA #> 20                                         NA                  NA #> 21                                         NA                  NA #> 22                                         NA                  NA #> 23                                         NA                  NA #> 24                                         NA                  NA #> 25                                         NA                  NA #> 26                                         NA                  NA #> 27                                         NA                  NA #>    text_validation_max identifier branching_logic required_field #> 1                   NA         NA              NA             NA #> 2                   NA         NA              NA             NA #> 3                   NA         NA              NA             NA #> 4                   NA         NA              NA             NA #> 5                   NA         NA              NA             NA #> 6                   NA         NA              NA             NA #> 7                   NA         NA              NA             NA #> 8                   NA         NA              NA             NA #> 9                   NA         NA              NA             NA #> 10                  NA         NA              NA             NA #> 11                  NA         NA              NA             NA #> 12                  NA         NA              NA             NA #> 13                  NA         NA              NA             NA #> 14                  NA         NA              NA             NA #> 15                  NA         NA              NA             NA #> 16                  NA         NA              NA             NA #> 17                  NA         NA              NA             NA #> 18                  NA         NA              NA             NA #> 19                  NA         NA              NA             NA #> 20                  NA         NA              NA             NA #> 21                  NA         NA              NA             NA #> 22                  NA         NA              NA             NA #> 23                  NA         NA              NA             NA #> 24                  NA         NA              NA             NA #> 25                  NA         NA              NA             NA #> 26                  NA         NA              NA             NA #> 27                  NA         NA              NA             NA #>    custom_alignment question_number matrix_group_name matrix_ranking #> 1                NA              NA                NA             NA #> 2                NA              NA                NA             NA #> 3                NA              NA                NA             NA #> 4                NA              NA                NA             NA #> 5                NA              NA                NA             NA #> 6                NA              NA                NA             NA #> 7                NA              NA                NA             NA #> 8                NA              NA                NA             NA #> 9                NA              NA                NA             NA #> 10               NA              NA                NA             NA #> 11               NA              NA                NA             NA #> 12               NA              NA                NA             NA #> 13               NA              NA                NA             NA #> 14               NA              NA                NA             NA #> 15               NA              NA                NA             NA #> 16               NA              NA                NA             NA #> 17               NA              NA                NA             NA #> 18               NA              NA                NA             NA #> 19               NA              NA                NA             NA #> 20               NA              NA                NA             NA #> 21               NA              NA                NA             NA #> 22               NA              NA                NA             NA #> 23               NA              NA                NA             NA #> 24               NA              NA                NA             NA #> 25               NA              NA                NA             NA #> 26               NA              NA                NA             NA #> 27               NA              NA                NA             NA #>    field_annotation #> 1                NA #> 2                NA #> 3                NA #> 4                NA #> 5                NA #> 6                NA #> 7                NA #> 8                NA #> 9                NA #> 10               NA #> 11               NA #> 12               NA #> 13               NA #> 14               NA #> 15               NA #> 16               NA #> 17               NA #> 18               NA #> 19               NA #> 20               NA #> 21               NA #> 22               NA #> 23               NA #> 24               NA #> 25               NA #> 26               NA #> 27               NA #>  #> $`Column names` #>  [1] \"record_id\"                    \"redcap_event_name\"            #>  [3] \"redcap_repeat_instrument\"     \"redcap_repeat_instance\"       #>  [5] \"cpr\"                          \"inclusion\"                    #>  [7] \"inclusion_time\"               \"dob\"                          #>  [9] \"age\"                          \"age_integer\"                  #> [11] \"sex\"                          \"cohabitation\"                 #> [13] \"hypertension\"                 \"diabetes\"                     #> [15] \"region\"                       \"baseline_data_start_complete\" #> [17] \"mrs_assessed\"                 \"mrs_date\"                     #> [19] \"mrs_score\"                    \"mrs_complete\"                 #> [21] \"con_mrs\"                      \"con_calc\"                     #> [23] \"consensus_complete\"           \"event_datetime\"               #> [25] \"event_age\"                    \"event_type\"                   #> [27] \"new_event_complete\"           #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract data from stata file for data dictionary — ds2dd_detailed","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"Extract data stata file data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"ds2dd_detailed(   data,   add.auto.id = FALSE,   date.format = \"dmy\",   form.name = NULL,   form.sep = NULL,   form.prefix = TRUE,   field.type = NULL,   field.label = NULL,   field.label.attr = \"label\",   field.validation = NULL,   metadata = names(REDCapCAST::redcapcast_meta),   convert.logicals = TRUE )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"data data frame add.auto.id flag add id column date.format date format, character string. ymd/dmy/mdy. dafault dmy. form.name manually specify form name(s). Vector length 1 ncol(data). Default NULL \"data\" used. form.sep supplied dataset form names suffix prefix column/variable names, seperator can specified. supplied, form.name ignored. Default NULL. form.prefix Flag set form prefix (TRUE) suffix (FALSE) column names. Assumes columns pre- suffix specified. field.type manually specify field type(s). Vector length 1 ncol(data). Default NULL \"text\" used everything factors, wil get \"radio\". field.label manually specify field label(s). Vector length 1 ncol(data). Default NULL colnames(data) used attribute `field.label.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). field.label.attr attribute name named labels haven_labelled data set (imported .dta file `haven::read_dta()`. Default \"label\" field.validation manually specify field validation(s). Vector length 1 ncol(data). Default NULL `levels()` used factors attribute `factor.labels.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). metadata redcap metadata headings. Default names(REDCapCAST::redcapcast_meta). convert.logicals convert logicals factor. Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"list length 2","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"function natural development ds2dd() function. assumes first column ID-column. checks. Please, always inspect data dictionary upload. Ensure, data set formatted much information possible. `field.type` can supplied","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"## Basic parsing with default options requireNamespace(\"REDCapCAST\") redcapcast_data |>   dplyr::select(-dplyr::starts_with(\"redcap_\")) |>   ds2dd_detailed() #> $data #> # A tibble: 25 × 24 #>    record_id cpr    inclusion  inclusion_time dob          age age_integer sex   #>        <dbl> <chr>  <date>     <chr>          <date>     <dbl>       <dbl> <chr> #>  1         1 12034… 2023-03-13 12:38:49       1940-03-12  83.0          83 fema… #>  2         2 01023… 2023-03-01 10:38:57       1934-02-01  89.1          89 male  #>  3         2 NA     NA         NA             NA          NA            NA NA    #>  4         2 NA     NA         NA             NA          NA            NA NA    #>  5         3 23015… 2022-03-08 12:01:07       1956-01-23  66.1          66 male  #>  6         3 NA     NA         NA             NA          NA            NA NA    #>  7         3 NA     NA         NA             NA          NA            NA NA    #>  8         3 NA     NA         NA             NA          NA            NA NA    #>  9         3 NA     NA         NA             NA          NA            NA NA    #> 10         3 NA     NA         NA             NA          NA            NA NA    #> # ℹ 15 more rows #> # ℹ 16 more variables: cohabitation <chr>, hypertension <chr>, diabetes <chr>, #> #   region <chr>, baseline_data_start_complete <chr>, mrs_assessed <chr>, #> #   mrs_date <date>, mrs_score <dbl>, mrs_complete <chr>, con_mrs <fct>, #> #   con_calc <fct>, consensus_complete <chr>, event_datetime <dttm>, #> #   event_age <dbl>, event_type <chr>, new_event_complete <chr> #>  #> $meta #> # A tibble: 24 × 18 #>    field_name     form_name section_header field_type field_label    #>    <chr>          <chr>     <lgl>          <chr>      <chr>          #>  1 record_id      data      NA             text       record_id      #>  2 cpr            data      NA             text       cpr            #>  3 inclusion      data      NA             text       inclusion      #>  4 inclusion_time data      NA             text       inclusion_time #>  5 dob            data      NA             text       dob            #>  6 age            data      NA             text       age            #>  7 age_integer    data      NA             text       age_integer    #>  8 sex            data      NA             text       sex            #>  9 cohabitation   data      NA             text       cohabitation   #> 10 hypertension   data      NA             text       hypertension   #> # ℹ 14 more rows #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\"        ## Adding a record_id field iris |> ds2dd_detailed(add.auto.id = TRUE) #> $data #> # A tibble: 150 × 6 #>    record_id sepal.length sepal.width petal.length petal.width species #>        <int>        <dbl>       <dbl>        <dbl>       <dbl> <fct>   #>  1         1          5.1         3.5          1.4         0.2 setosa  #>  2         2          4.9         3            1.4         0.2 setosa  #>  3         3          4.7         3.2          1.3         0.2 setosa  #>  4         4          4.6         3.1          1.5         0.2 setosa  #>  5         5          5           3.6          1.4         0.2 setosa  #>  6         6          5.4         3.9          1.7         0.4 setosa  #>  7         7          4.6         3.4          1.4         0.3 setosa  #>  8         8          5           3.4          1.5         0.2 setosa  #>  9         9          4.4         2.9          1.4         0.2 setosa  #> 10        10          4.9         3.1          1.5         0.1 setosa  #> # ℹ 140 more rows #>  #> $meta #> # A tibble: 6 × 18 #>   field_name   form_name section_header field_type field_label  #>   <chr>        <chr>     <lgl>          <chr>      <chr>        #> 1 record_id    data      NA             text       record_id    #> 2 sepal.length data      NA             text       Sepal.Length #> 3 sepal.width  data      NA             text       Sepal.Width  #> 4 petal.length data      NA             text       Petal.Length #> 5 petal.width  data      NA             text       Petal.Width  #> 6 species      data      NA             radio      Species      #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\"        ## Passing form name information to function iris |>   ds2dd_detailed(     add.auto.id = TRUE,     form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2))   ) |>   purrr::pluck(\"meta\") #> # A tibble: 6 × 18 #>   field_name   form_name section_header field_type field_label  #>   <chr>        <chr>     <lgl>          <chr>      <chr>        #> 1 record_id    b         NA             text       record_id    #> 2 sepal.length c         NA             text       Sepal.Length #> 3 sepal.width  b         NA             text       Sepal.Width  #> 4 petal.length c         NA             text       Petal.Length #> 5 petal.width  b         NA             text       Petal.Width  #> 6 species      c         NA             radio      Species      #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> mtcars |> ds2dd_detailed(add.auto.id = TRUE) #> $data #> # A tibble: 32 × 12 #>    record_id   mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb #>        <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1         1  21       6  160    110  3.9   2.62  16.5     0     1     4     4 #>  2         2  21       6  160    110  3.9   2.88  17.0     0     1     4     4 #>  3         3  22.8     4  108     93  3.85  2.32  18.6     1     1     4     1 #>  4         4  21.4     6  258    110  3.08  3.22  19.4     1     0     3     1 #>  5         5  18.7     8  360    175  3.15  3.44  17.0     0     0     3     2 #>  6         6  18.1     6  225    105  2.76  3.46  20.2     1     0     3     1 #>  7         7  14.3     8  360    245  3.21  3.57  15.8     0     0     3     4 #>  8         8  24.4     4  147.    62  3.69  3.19  20       1     0     4     2 #>  9         9  22.8     4  141.    95  3.92  3.15  22.9     1     0     4     2 #> 10        10  19.2     6  168.   123  3.92  3.44  18.3     1     0     4     4 #> # ℹ 22 more rows #>  #> $meta #> # A tibble: 12 × 18 #>    field_name form_name section_header field_type field_label #>    <chr>      <chr>     <lgl>          <chr>      <chr>       #>  1 record_id  data      NA             text       record_id   #>  2 mpg        data      NA             text       mpg         #>  3 cyl        data      NA             text       cyl         #>  4 disp       data      NA             text       disp        #>  5 hp         data      NA             text       hp          #>  6 drat       data      NA             text       drat        #>  7 wt         data      NA             text       wt          #>  8 qsec       data      NA             text       qsec        #>  9 vs         data      NA             text       vs          #> 10 am         data      NA             text       am          #> 11 gear       data      NA             text       gear        #> 12 carb       data      NA             text       carb        #> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\"        ## Using column name suffix to carry form name data <- iris |>   ds2dd_detailed(add.auto.id = TRUE) |>   purrr::pluck(\"data\") names(data) <- glue::glue(\"{sample(x = c('a','b'),size = length(names(data)), replace=TRUE,prob = rep(x=.5,2))}__{names(data)}\") data |> ds2dd_detailed(form.sep = \"__\") #> $data #> # A tibble: 150 × 6 #>    record_id sepal.length sepal.width petal.length petal.width species #>        <int>        <dbl>       <dbl>        <dbl>       <dbl> <fct>   #>  1         1          5.1         3.5          1.4         0.2 setosa  #>  2         2          4.9         3            1.4         0.2 setosa  #>  3         3          4.7         3.2          1.3         0.2 setosa  #>  4         4          4.6         3.1          1.5         0.2 setosa  #>  5         5          5           3.6          1.4         0.2 setosa  #>  6         6          5.4         3.9          1.7         0.4 setosa  #>  7         7          4.6         3.4          1.4         0.3 setosa  #>  8         8          5           3.4          1.5         0.2 setosa  #>  9         9          4.4         2.9          1.4         0.2 setosa  #> 10        10          4.9         3.1          1.5         0.1 setosa  #> # ℹ 140 more rows #>  #> $meta #> # A tibble: 6 × 18 #>   field_name   form_name section_header field_type field_label  #>   <chr>        <chr>     <lgl>          <chr>      <chr>        #> 1 record_id    b         NA             text       record_id    #> 2 sepal.length a         NA             text       sepal.length #> 3 sepal.width  b         NA             text       sepal.width  #> 4 petal.length a         NA             text       petal.length #> 5 petal.width  b         NA             text       petal.width  #> 6 species      a         NA             radio      species      #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"Secure API key storage and data acquisition in one — easy_redcap","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"Secure API key storage data acquisition one","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"","code":"easy_redcap(project.name, widen.data = TRUE, uri, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"project.name name current project (key storage `keyring::key_set()`, using default keyring) widen.data argument widen exported data uri REDCap database API uri ... arguments passed `REDCapCAST::read_redcap_tables()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"data.frame list depending widen.data","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"Metadata can added editing data dictionary project initial design phase. want later add new instruments, function can used create () instrument(s) add project production.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"","code":"export_redcap_instrument(data, file, force = FALSE, record.id = \"record_id\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"data metadata relevant instrument. `ds2dd_detailed()` file destination file name. force force instrument creation ignore different form names just using first. record.id record id variable name. Default 'record_id'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"exports zip-file","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"","code":"# iris |> #  ds2dd_detailed( #    add.auto.id = TRUE, #    form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2)) #  ) |> #  purrr::pluck(\"meta\") |> #  (\\(.x){ #  split(.x, .x$form_name) #  })() |> #  purrr::imap(function(.x, .i){ #  export_redcap_instrument(.x,file=here::here(paste0(.i,Sys.Date(),\".zip\"))) #  })  # iris |> #  ds2dd_detailed( #    add.auto.id = TRUE #  ) |> #  purrr::pluck(\"meta\") |> #  export_redcap_instrument(file=here::here(paste0(\"instrument\",Sys.Date(),\".zip\")))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":null,"dir":"Reference","previous_headings":"","what":"Allows conversion of factor to numeric values preserving original levels — fct2num","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"Allows conversion factor numeric values preserving original levels","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"","code":"fct2num(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"numeric vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"","code":"c(1, 4, 3, \"A\", 7, 8, 1) |>   as_factor() |>   fct2num() #> Warning: invalid roman numeral: A #> [1] 1 2 3 4 5 6 1  structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |>   as_factor() |>   fct2num() #> [1]  1  2  3  2 10  9  structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"labelled\" ) |>   as_factor() |>   fct2num() #> [1]  1  2  3  2 10  9  # Outlier with labels, but no class of origin, handled like numeric vector # structure(c(1, 2, 3, 2, 10, 9), #   labels = c(Unknown = 9, Refused = 10) # ) |> #   as_factor() |> #   fct2num()  v <- sample(6:19, 20, TRUE) |> factor() dput(v) #> structure(c(7L, 1L, 10L, 3L, 10L, 10L, 9L, 8L, 3L, 2L, 6L, 8L,  #> 3L, 5L, 4L, 8L, 1L, 6L, 5L, 5L), levels = c(\"6\", \"7\", \"8\", \"9\",  #> \"11\", \"12\", \"13\", \"15\", \"16\", \"17\"), class = \"factor\") named_levels(v) #> 13  6 17  8 16 15  7 12 11  9  #>  7  1 10  3  9  8  2  6  5  4  fct2num(v) #>  [1] 13  6 17  8 17 17 16 15  8  7 12 15  8 11  9 15  6 12 11 11"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop unused levels preserving label data — fct_drop","title":"Drop unused levels preserving label data — fct_drop","text":"extends [forcats::fct_drop()] natively work across data.frame replace [base::droplevels()].","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop unused levels preserving label data — fct_drop","text":"","code":"fct_drop.data.frame(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop unused levels preserving label data — fct_drop","text":"x Factor drop unused levels ... arguments passed method.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRECATED Helper to import files correctly — file_extension","title":"DEPRECATED Helper to import files correctly — file_extension","text":"DEPRECATED Helper import files correctly","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRECATED Helper to import files correctly — file_extension","text":"","code":"file_extension(filenames)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRECATED Helper to import files correctly — file_extension","text":"filenames file names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRECATED Helper to import files correctly — file_extension","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DEPRECATED Helper to import files correctly — file_extension","text":"","code":"file_extension(list.files(here::here(\"\"))[[2]])[[1]] #> [1] \"\" file_extension(c(\"file.cd..ks\", \"file\")) #> [1] \"ks\" \"\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"focused_metadata — focused_metadata","title":"focused_metadata — focused_metadata","text":"Extracts limited metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"focused_metadata — focused_metadata","text":"","code":"focused_metadata(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"focused_metadata — focused_metadata","text":"metadata dataframe containing metadata vars_in_data Vector variable names dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"focused_metadata — focused_metadata","text":"dataframe containing metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":null,"dir":"Reference","previous_headings":"","what":"Sub-header formatting wrapper — format_subheader","title":"Sub-header formatting wrapper — format_subheader","text":"Sub-header formatting wrapper","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sub-header formatting wrapper — format_subheader","text":"","code":"format_subheader(data, tag = \"h2\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sub-header formatting wrapper — format_subheader","text":"data character vector tag character vector length 1","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sub-header formatting wrapper — format_subheader","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sub-header formatting wrapper — format_subheader","text":"","code":"\"Instrument header\" |> format_subheader() #> <div class=\"rich-text-field-label\"><h2>Instrument header<\/h2><\/div>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"Retrieve project API key stored, , set retrieve","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"","code":"get_api_key(key.name)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"key.name character vector key name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract attribute. Returns NA if none — get_attr","title":"Extract attribute. Returns NA if none — get_attr","text":"Extract attribute. Returns NA none","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract attribute. Returns NA if none — get_attr","text":"","code":"get_attr(data, attr = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract attribute. Returns NA if none — get_attr","text":"data vector attr attribute name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract attribute. Returns NA if none — get_attr","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract attribute. Returns NA if none — get_attr","text":"","code":"attr(mtcars$mpg, \"label\") <- \"testing\" do.call(c, sapply(mtcars, get_attr)) #> $mpg.label #> [1] \"testing\" #>  if (FALSE) { # \\dontrun{ mtcars |>   numchar2fct(numeric.threshold = 6) |>   ds2dd_detailed() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the id name — get_id_name","title":"Get the id name — get_id_name","text":"Get id name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the id name — get_id_name","text":"","code":"get_id_name(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the id name — get_id_name","text":"data data frame list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the id name — get_id_name","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess time variables based on naming pattern — guess_time_only","title":"Guess time variables based on naming pattern — guess_time_only","text":"repairing data time variables appended \"1970-01-01\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess time variables based on naming pattern — guess_time_only","text":"","code":"guess_time_only(   data,   validate.time = FALSE,   time.var.sel.pos = \"[Tt]i[d(me)]\",   time.var.sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess time variables based on naming pattern — guess_time_only","text":"data data.frame tibble validate.time Flag validate guessed time columns time.var.sel.pos Positive selection regex string passed `gues_time_only_filter()` sel.pos. time.var.sel.neg Negative selection regex string passed `gues_time_only_filter()` sel.neg.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess time variables based on naming pattern — guess_time_only","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Guess time variables based on naming pattern — guess_time_only","text":"","code":"redcapcast_data |> guess_time_only(validate.time = TRUE) #> $is.POSIX #> # A tibble: 25 × 2 #>    inclusion_time event_datetime      #>    <time>         <dttm>              #>  1 12:38:49       NA                  #>  2 10:38:57       NA                  #>  3       NA       NA                  #>  4       NA       2024-01-18 12:49:42 #>  5 12:01:07       NA                  #>  6       NA       NA                  #>  7       NA       NA                  #>  8       NA       2024-01-18 12:49:58 #>  9       NA       2024-01-18 12:50:01 #> 10       NA       2024-01-18 12:50:05 #> # ℹ 15 more rows #>  #> $is.datetime #> # A tibble: 25 × 1 #>    event_datetime      #>    <dttm>              #>  1 NA                  #>  2 NA                  #>  3 NA                  #>  4 2024-01-18 12:49:42 #>  5 NA                  #>  6 NA                  #>  7 NA                  #>  8 2024-01-18 12:49:58 #>  9 2024-01-18 12:50:01 #> 10 2024-01-18 12:50:05 #> # ℹ 15 more rows #>  #> $is.time_only #> # A tibble: 25 × 1 #>    inclusion_time #>    <time>         #>  1 12:38:49       #>  2 10:38:57       #>  3       NA       #>  4       NA       #>  5 12:01:07       #>  6       NA       #>  7       NA       #>  8       NA       #>  9       NA       #> 10       NA       #> # ℹ 15 more rows #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Try at determining which are true time only variables — guess_time_only_filter","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"just try guessing data type based data class column names hoping tiny bit naming consistency. R include time-data format natively, \"hms\" class `readr` used. converted character class REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"guess_time_only_filter(   data,   validate = FALSE,   sel.pos = \"[Tt]i[d(me)]\",   sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"data data set validate flag output validation data. output list. sel.pos Positive selection regex string sel.neg Negative selection regex string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"character vector list depending `validate` flag.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"data <- redcapcast_data data |> guess_time_only_filter() #> [1] \"inclusion_time\" data |>   guess_time_only_filter(validate = TRUE) |>   lapply(head) #> $is.POSIX #> # A tibble: 6 × 2 #>   inclusion_time event_datetime      #>   <time>         <dttm>              #> 1 12:38:49       NA                  #> 2 10:38:57       NA                  #> 3       NA       NA                  #> 4       NA       2024-01-18 12:49:42 #> 5 12:01:07       NA                  #> 6       NA       NA                  #>  #> $is.datetime #> # A tibble: 6 × 1 #>   event_datetime      #>   <dttm>              #> 1 NA                  #> 2 NA                  #> 3 NA                  #> 4 2024-01-18 12:49:42 #> 5 NA                  #> 6 NA                  #>  #> $is.time_only #> # A tibble: 6 × 1 #>   inclusion_time #>   <time>         #> 1 12:38:49       #> 2 10:38:57       #> 3       NA       #> 4       NA       #> 5 12:01:07       #> 6       NA       #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"Finish incomplete haven attributes substituting missings values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"","code":"haven_all_levels(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"data haven labelled variable","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"","code":"ds <- structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) haven::is.labelled(ds) #> [1] TRUE attributes(ds) #> $labels #> Unknown Refused  #>       9      10  #>  #> $class #> [1] \"haven_labelled\" #>  ds |> haven_all_levels() #>       1       2       3 Unknown Refused  #>       1       2       3       9      10"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":null,"dir":"Reference","previous_headings":"","what":"Change ","title":"Change ","text":"Change \"hms\" \"character\" REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change ","text":"","code":"hms2character(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change ","text":"data data set","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change ","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change ","text":"","code":"data <- redcapcast_data ## data |> time_only_correction() |> hms2character()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"Simple html tag wrapping REDCap text formatting","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"","code":"html_tag_wrap(data, tag = \"h2\", extra = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"data character vector tag character vector length 1 extra character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"","code":"html_tag_wrap(\"Titel\", tag = \"div\", extra = 'class=\"rich-text-field-label\"') #> <div class=\"rich-text-field-label\">Titel<\/div> html_tag_wrap(\"Titel\", tag = \"h2\") #> <h2>Titel<\/h2>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for multiple label classes — is.labelled","title":"Tests for multiple label classes — is.labelled","text":"Tests multiple label classes","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for multiple label classes — is.labelled","text":"","code":"is.labelled(   x,   classes = c(\"redcapcast_labelled\", \"haven_labelled\", \"labelled\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for multiple label classes — is.labelled","text":"x data classes classes test","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for multiple label classes — is.labelled","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tests for multiple label classes — is.labelled","text":"","code":"structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |> is.labelled() #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":null,"dir":"Reference","previous_headings":"","what":"Multi missing check — is_missing","title":"Multi missing check — is_missing","text":"Multi missing check","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multi missing check — is_missing","text":"","code":"is_missing(data, nas = c(\"\", \"NA\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multi missing check — is_missing","text":"data character vector nas character vector strings considered NA","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multi missing check — is_missing","text":"logical vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if repeatable or longitudinal — is_repeated_longitudinal","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"Test repeatable longitudinal","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(   data,   generics = c(\"redcap_event_name\", \"redcap_repeat_instrument\", \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"data data set generics default \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(c(\"record_id\", \"age\", \"record_id\", \"gender\")) #> [1] FALSE is_repeated_longitudinal(redcapcast_data) #> [1] TRUE is_repeated_longitudinal(list(redcapcast_data)) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":null,"dir":"Reference","previous_headings":"","what":"Completion marking based on completed upload — mark_complete","title":"Completion marking based on completed upload — mark_complete","text":"Completion marking based completed upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Completion marking based on completed upload — mark_complete","text":"","code":"mark_complete(upload, ls)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Completion marking based on completed upload — mark_complete","text":"upload output list `REDCapR::redcap_write()` ls output list `ds2dd_detailed()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Completion marking based on completed upload — mark_complete","text":"list `REDCapR::redcap_write()` results","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":null,"dir":"Reference","previous_headings":"","what":"Match fields to forms — match_fields_to_form","title":"Match fields to forms — match_fields_to_form","text":"Match fields forms","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match fields to forms — match_fields_to_form","text":"","code":"match_fields_to_form(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match fields to forms — match_fields_to_form","text":"metadata data frame containing field names form names vars_in_data character vector variable names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match fields to forms — match_fields_to_form","text":"data frame containing field names form names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"mtcars dataset slightly modified use Shiny app upload demonstration","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"","code":"data(mtcars_redcap)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"data frame 13 variables: record_id ID, numeric mpg ID, numeric cyl ID, numeric disp ID, numeric hp ID, numeric drat ID, numeric wt ID, numeric qsec ID, numeric vs ID, numeric ID, numeric gear ID, numeric carb ID, numeric name original rownames, charater","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get named vector of factor levels and values — named_levels","title":"Get named vector of factor levels and values — named_levels","text":"Get named vector factor levels values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get named vector of factor levels and values — named_levels","text":"","code":"named_levels(data, label = \"labels\", na.label = NULL, na.value = 99)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get named vector of factor levels and values — named_levels","text":"data factor label character string attribute named vector factor labels na.label character string refactor NA values. Default NULL. na.value new value NA strings. Ignored na.label NULL. Default 99.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get named vector of factor levels and values — named_levels","text":"named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get named vector of factor levels and values — named_levels","text":"","code":"if (FALSE) { # \\dontrun{ structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |>   as_factor() |>   named_levels() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":null,"dir":"Reference","previous_headings":"","what":"Nav_bar defining function for shiny ui — nav_bar_page","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"Nav_bar defining function shiny ui","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"","code":"nav_bar_page()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"shiny object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Applying var2fct across data set — numchar2fct","title":"Applying var2fct across data set — numchar2fct","text":"Individual thresholds character numeric columns","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applying var2fct across data set — numchar2fct","text":"","code":"numchar2fct(data, numeric.threshold = 6, character.throshold = 6)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applying var2fct across data set — numchar2fct","text":"data dataset. data.frame tibble numeric.threshold threshold var2fct numeric columns. Default 6. character.throshold threshold var2fct character columns. Default 6.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applying var2fct across data set — numchar2fct","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Applying var2fct across data set — numchar2fct","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ... if (FALSE) { # \\dontrun{ mtcars |>   numchar2fct(numeric.threshold = 6) |>   str() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper to auto-parse un-formatted data with haven and readr — parse_data","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"Helper auto-parse un-formatted data haven readr","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"","code":"parse_data(   data,   guess_type = TRUE,   col_types = NULL,   locale = readr::default_locale(),   ignore.vars = \"cpr\",   ... )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"data data.frame tibble guess_type logical guess type readr col_types specify col_types using readr semantics. Ignored guess_type TRUE locale option specify locale. Defaults readr::default_locale(). ignore.vars specify column names columns ignore parsing ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"","code":"mtcars |>   parse_data() |>   str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if vector can be interpreted as roman numerals — possibly_roman","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"Test vector can interpreted roman numerals","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"","code":"possibly_roman(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"data character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"","code":"sample(1:100, 10) |>   as.roman() |>   possibly_roman() #> [1] TRUE sample(c(TRUE, FALSE), 10, TRUE) |> possibly_roman() #> [1] FALSE rep(NA, 10) |> possibly_roman() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing character — process_user_input.character","title":"User input processing character — process_user_input.character","text":"User input processing character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing character — process_user_input.character","text":"","code":"# S3 method for class 'character' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing character — process_user_input.character","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing character — process_user_input.character","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing data.frame — process_user_input.data.frame","title":"User input processing data.frame — process_user_input.data.frame","text":"User input processing data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing data.frame — process_user_input.data.frame","text":"","code":"# S3 method for class 'data.frame' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing data.frame — process_user_input.data.frame","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing data.frame — process_user_input.data.frame","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing default — process_user_input.default","title":"User input processing default — process_user_input.default","text":"User input processing default","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing default — process_user_input.default","text":"","code":"# Default S3 method process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing default — process_user_input.default","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing default — process_user_input.default","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing — process_user_input","title":"User input processing — process_user_input","text":"User input processing","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing — process_user_input","text":"","code":"process_user_input(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing — process_user_input","text":"x input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing — process_user_input","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing response — process_user_input.response","title":"User input processing response — process_user_input.response","text":"User input processing response","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing response — process_user_input.response","text":"","code":"# S3 method for class 'response' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing response — process_user_input.response","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing response — process_user_input.response","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #>       id    ab   age   imm   vis   ver   att   del #>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1     1     1    74    38    35    30    29    35 #>  2     1     2    69    36    36    21    27    37 #>  3     2     1    63    32    31    26    34    38 #>  4     2     2    64    37    34    26    36    46 #>  5     3     1    69    39    33    31    47    29 #>  6     3     2    70    40    36    31    46    25 #>  7     4     1    79    44    37    20    37    36 #>  8     4     2    81    35    36    31    37    40 #>  9     5     1    77    35    26    17    20    36 #> 10     5     2    80    29    34    18    23    36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"Convenience function download complete instrument, using token storage keyring.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"","code":"read_redcap_instrument(   key,   uri,   instrument,   raw_or_label = \"raw\",   id_name = \"record_id\",   records = NULL )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"key key name standard keyring token retrieval. uri REDCap database API uri instrument instrument name raw_or_label raw label passed `REDCapR::redcap_read()` id_name id variable name. Default \"record_id\". records specify records download. Index numbers. Numeric vector.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Download REDCap data — read_redcap_tables","title":"Download REDCap data — read_redcap_tables","text":"Implementation REDCap_split focused data acquisition approach using REDCapR::redcap_read downloading specified fields, forms /events using built-focused_metadata including clean-. Works classical longitudinal projects without repeating instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download REDCap data — read_redcap_tables","text":"","code":"read_redcap_tables(   uri,   token,   records = NULL,   fields = NULL,   events = NULL,   forms = NULL,   raw_or_label = \"label\",   split_forms = \"all\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download REDCap data — read_redcap_tables","text":"uri REDCap database API uri token API token records records download fields fields download events events download forms forms download raw_or_label raw label tags. Can * \"raw\": Standard [REDCapR] method get raw values.   * \"label\": Standard [REDCapR] method get label values.   * \"\": Get raw values REDCap labels applied labels. Use   [as_factor()] format factors original labels use   [gtsummary] package easily get beautiful tables original labels   REDCap. Use [fct_drop()] drop empty levels. split_forms Whether split \"repeating\" \"\" forms, default .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download REDCap data — read_redcap_tables","text":"list instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download REDCap data — read_redcap_tables","text":"","code":"# Examples will be provided later"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":null,"dir":"Reference","previous_headings":"","what":"Redcap Wider — redcap_wider","title":"Redcap Wider — redcap_wider","text":"Converts list REDCap data frames long wide format. Handles longitudinal projects, yet repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Redcap Wider — redcap_wider","text":"","code":"redcap_wider(   data,   event.glue = \"{.value}_{redcap_event_name}\",   inst.glue = \"{.value}_{redcap_repeat_instance}\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Redcap Wider — redcap_wider","text":"data list data frames. event.glue dplyr::glue string repeated events naming inst.glue dplyr::glue string repeated instruments naming","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Redcap Wider — redcap_wider","text":"list data frames wide format.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Redcap Wider — redcap_wider","text":"","code":"# Longitudinal list1 <- list(   data.frame(     record_id = c(1, 2, 1, 2),     redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"),     age = c(25, 26, 27, 28)   ),   data.frame(     record_id = c(1, 2),     redcap_event_name = c(\"baseline\", \"baseline\"),     gender = c(\"male\", \"female\")   ) ) redcap_wider(list1) #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup gender #> 1         1           25           27   male #> 2         2           26           28 female # Simpel with two instruments list2 <- list(   data.frame(     record_id = c(1, 2),     age = c(25, 26)   ),   data.frame(     record_id = c(1, 2),     gender = c(\"male\", \"female\")   ) ) redcap_wider(list2) #> Joining with `by = join_by(record_id)` #>   record_id age gender #> 1         1  25   male #> 2         2  26 female # Simple with single instrument list3 <- list(data.frame(   record_id = c(1, 2),   age = c(25, 26) )) redcap_wider(list3) #>   record_id age #> 1         1  25 #> 2         2  26 # Longitudinal with repeatable instruments list4 <- list(   data.frame(     record_id = c(1, 2, 1, 2),     redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"),     age = c(25, 26, 27, 28)   ),   data.frame(     record_id = c(1, 1, 1, 1, 2, 2, 2, 2),     redcap_event_name = c(       \"baseline\", \"baseline\", \"followup\", \"followup\",       \"baseline\", \"baseline\", \"followup\", \"followup\"     ),     redcap_repeat_instrument = \"walk\",     redcap_repeat_instance = c(1, 2, 1, 2, 1, 2, 1, 2),     dist = c(40, 32, 25, 33, 28, 24, 23, 36)   ),   data.frame(     record_id = c(1, 2),     redcap_event_name = c(\"baseline\", \"baseline\"),     gender = c(\"male\", \"female\")   ) ) redcap_wider(list4) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup dist_1_baseline dist_1_followup #> 1         1           25           27              40              25 #> 2         2           26           28              28              23 #>   dist_2_baseline dist_2_followup gender #> 1              32              33   male #> 2              24              36 female"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data set for demonstration — redcapcast_data","title":"Data set for demonstration — redcapcast_data","text":"small dataset REDCap database demonstrational purposes. Contains synthetic data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data set for demonstration — redcapcast_data","text":"","code":"data(redcapcast_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data set for demonstration — redcapcast_data","text":"data frame 22 variables: record_id ID, numeric redcap_event_name Event name, character redcap_repeat_instrument Repeat instrument, character redcap_repeat_instance Repeat instance, numeric cpr CPR number, character inclusion Inclusion date, Date inclusion_time Inclusion time, hms dob Date birth, Date age Age decimal, numeric age_integer Age integer, numeric sex Legal sex, character cohabitation Cohabitation status, character con_calc con_calc con_mrs con_mrs consensus_complete consensus_complete hypertension Hypertension, character diabetes diabetes, character region region, character baseline_data_start_complete Completed, character mrs_assessed mRS Assessed, character mrs_date Assesment date, Date mrs_score Categorical score, numeric mrs_complete Complete, numeric event_datetime Event datetime, POSIXct event_age Age time event, numeric event_type Event type, character new_event_complete Completed, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCap metadata from data base — redcapcast_meta","title":"REDCap metadata from data base — redcapcast_meta","text":"metadata dataset REDCap database demonstration purposes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"REDCap metadata from data base — redcapcast_meta","text":"","code":"data(redcapcast_meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"REDCap metadata from data base — redcapcast_meta","text":"data frame 22 variables: field_name field_name, character form_name form_name, character section_header section_header, character field_type field_type, character field_label field_label, character select_choices_or_calculations select_choices_or_calculations, character field_note field_note, character text_validation_type_or_show_slider_number text_validation_type_or_show_slider_number, character text_validation_min text_validation_min, character text_validation_max text_validation_max, character identifier identifier, character branching_logic branching_logic, character required_field required_field, character custom_alignment custom_alignment, character question_number question_number, character matrix_group_name matrix_group_name, character matrix_ranking matrix_ranking, character field_annotation field_annotation, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace curly apostrophes and quotes from word — replace_curly_quote","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"Copied textclean, updated since 2018 CRAN. Github:https://github.com/trinker/textclean","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"","code":"replace_curly_quote(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"x character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Sanitize list of data frames — sanitize_split","title":"Sanitize list of data frames — sanitize_split","text":"Removing empty rows","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sanitize list of data frames — sanitize_split","text":"","code":"sanitize_split(   l,   generic.names = c(\"redcap_event_name\", \"redcap_repeat_instrument\",     \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sanitize list of data frames — sanitize_split","text":"l list data frames. generic.names vector generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sanitize list of data frames — sanitize_split","text":"list data frames generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Set attributes for named attribute. Appends if attr is NULL — set_attr","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"Set attributes named attribute. Appends attr NULL","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"","code":"set_attr(data, label, attr = NULL, overwrite = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"data vector label label attr attribute name overwrite overwrite existing attributes. Default FALSE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"vector attribute","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the included Shiny-app for database casting and upload — shiny_cast","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"Wraps shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"shiny_cast(...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"... Arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"# shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a data frame into separate tables for each form — split_non_repeating_forms","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"Split data frame separate tables form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"split_non_repeating_forms(table, universal_fields, fields)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"table data frame universal_fields character vector fields included every table fields two-column matrix containing names fields included form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"list data frames, one non-repeating form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"# Create a table table <- data.frame(   id = c(1, 2, 3, 4, 5),   form_a_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_a_age = c(25, 30, 25, 15, 20),   form_b_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_b_gender = c(\"M\", \"F\", \"M\", \"F\", \"F\") )  # Create the universal fields universal_fields <- c(\"id\")  # Create the fields fields <- matrix(   c(     \"form_a_name\", \"form_a\",     \"form_a_age\", \"form_a\",     \"form_b_name\", \"form_b\",     \"form_b_gender\", \"form_b\"   ),   ncol = 2, byrow = TRUE )  # Split the table split_non_repeating_forms(table, universal_fields, fields) #> $form_a_age #>   id #> 1  1 #> 2  2 #> 3  3 #> 4  4 #> 5  5 #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended string splitting — strsplitx","title":"Extended string splitting — strsplitx","text":"Can used substitute base function. Main claim fame easing split around defined delimiter, see example.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended string splitting — strsplitx","text":"","code":"strsplitx(x, split, type = \"classic\", perl = FALSE, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended string splitting — strsplitx","text":"x data split delimiter type Split type. Can c(\"classic\", \"\", \"\", \"around\") perl perl param strsplit() ... additional parameters passed base strsplit handling splits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended string splitting — strsplitx","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended string splitting — strsplitx","text":"","code":"test <- c(\"12 months follow-up\", \"3 steps\", \"mRS 6 weeks\", \"Counting to 231 now\") strsplitx(test, \"[0-9]\", type = \"around\") #> [[1]] #> [1] \"1\"                 \"2\"                 \" months follow-up\" #>  #> [[2]] #> [1] \"3\"      \" steps\" #>  #> [[3]] #> [1] \"mRS \"   \"6\"      \" weeks\" #>  #> [[4]] #> [1] \"Counting to \" \"2\"            \"3\"            \"1\"            \" now\"         #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":null,"dir":"Reference","previous_headings":"","what":"Correction based on time_only_filter function — time_only_correction","title":"Correction based on time_only_filter function — time_only_correction","text":"Correction based time_only_filter function","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correction based on time_only_filter function — time_only_correction","text":"","code":"time_only_correction(data, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correction based on time_only_filter function — time_only_correction","text":"data data set ... arguments passed `guess_time_only_filter()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correction based on time_only_filter function — time_only_correction","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correction based on time_only_filter function — time_only_correction","text":"","code":"data <- redcapcast_data ## data |> time_only_correction()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert vector to factor based on threshold of number of unique levels — var2fct","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"wrapper forcats::as_factor, sorts numeric vectors factoring, levels character vectors order appearance.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"","code":"var2fct(data, unique.n)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"data vector data.frame column unique.n threshold convert class factor","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"","code":"sample(seq_len(4), 20, TRUE) |>   var2fct(6) |>   summary() #> 1 2 3 4  #> 9 2 6 3  sample(letters, 20) |>   var2fct(6) |>   summary() #>    Length     Class      Mode  #>        20 character character  sample(letters[1:4], 20, TRUE) |> var2fct(6) #> Warning: invalid roman numerals: a b a a a a b #>  [1] c d c d a b d a d c a d a c c a b c d c #> Levels: c d a b"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"Named vector REDCap choices (`wrapping compact_vec()`)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"","code":"vec2choice(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"data named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"character string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"","code":"sample(seq_len(4), 20, TRUE) |>   as_factor() |>   named_levels() |>   sort() |>   vec2choice() #> [1] \"1, 1 | 2, 2 | 3, 3 | 4, 4\""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24114","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.4","title":"REDCapCAST 24.11.4","text":"hosting shinyapps.io given lot trouble recently. Modyfied package structure little around shiny_cast(), accommodate alternative hosting approach package functions included script instead requiring package. NEW: new option raw_or_label read_readcap_tables() added: “”. Get raw values REDCap labels applied labels. Use as_factor() format factors original labels use gtsummary package easily get beautiful tables original labels REDCap. Use fct_drop() drop empty levels. NEW: fct_drop() added extension forcats::fct_drop(), works across data.frames. Use fct_drop(). CHANGE: default data export method easy_redcap() changed use new labelled data export read_readcap_tables().","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24113","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.3","title":"REDCapCAST 24.11.3","text":"BUG: shiny_cast() fails load missed loading REDCapCAST library ui.r. Fixed. Tests great.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24112","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.2","title":"REDCapCAST 24.11.2","text":"CRAN release: 2024-11-22 24.11.1 rejected CRAN based wrong title capitalisation. opportunity extend package overhaul. actually turned major step towards usable shiny app received focus. implemented option specify categorical variables factorize, modified version {forcats} {haven}’s as_factor(), preserve attributes applied data able upload cast REDCap meta data richly formatted data (use .rds). matter input type, input parsed using default options {readr} package. Also avoid mis-labelling, logicals converted factors REDCap truefalse class follows different naming conversion compared R. Also correct support variable labels field labels (use .rds formatted data label labelled::var_label()) Vignettes documentation restructured. package detached REDCapRITS, originally forked . data split function kept, testing rewritten. projects evolved away original fork.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24111","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.1","title":"REDCapCAST 24.11.1","text":"Revised tests. Documentation slightly updated highlight shiny app casting REDCap metadata. working hosting Shiny Server.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-11-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 24.11.1","text":"Bug: ‘form.name’ specified ‘ds2dd_detailed()’ ignored. Corrected ignored ‘form.sep’ specified. Added handling re-occurring form.sep pattern. New: export_redcap_instrument() new version create_instrument_meta(), export single instrument. Multiple instrument export can done lapply() purrr::map(). allows inclusion functionality Shiny implementation easier handle. create_instrument_meta() deprecated. Improved: shiny_cast() app updated actually work install package clones whole repository.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"shiny-24-11-1","dir":"Changelog","previous_headings":"","what":"Shiny:","title":"REDCapCAST 24.11.1","text":"New: Major overhaul app interface introduction bslib building page. Also Detailed documentation added app workflow. New: Export REDCap instrument ready add database based uploaded spreadsheet. thanks export_redcap_instrument() function. functionality intended projects production adding instruments handled manually API upload. Bug: Export datadictionary “” instead “NA” NAs. Upload REDCap failed. anymore. shiny implementation included package. Implementing shinylive may looked later.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24103","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.10.3","title":"REDCapCAST 24.10.3","text":"CRAN release: 2024-10-03 Updated links spelling.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24101","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.10.1","title":"REDCapCAST 24.10.1","text":"Minor changes pass tests renv . rhub really running smooth previously.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2461","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.6.1","title":"REDCapCAST 24.6.1","text":"CRAN release: 2024-06-07","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-6-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.6.1","text":"Fix: read_redcap_tables(): field names testing allows include “[form_name]_complete” fields. Fix: ds2dd_detailed(): default record ID name now “record_id”, REDCap default. Default still use first column name. Support added interpret column name prefix suffix instrument names. See examples. New: create_instrument_meta(): creates zip instrument files allow adding new instruments project production. Takes data dictionary input creates zip instrument specified form_name column. New: doc2dd(): function convert document table data dictionary. allows specify instrument whole data dictionary text document, easier work easily modifiable. generic case data frame variable names values column. format like REDCap data dictionary, gives options formatting. related functions data handling formatting. One interesting function case_match_regex_list(), allows dynamic dplyr::case_when()-like approach regex-matching. think neat least.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-and-more-24-6-1","dir":"Changelog","previous_headings":"","what":"Documentation and more","title":"REDCapCAST 24.6.1","text":"Dependencies: order deploy shiny_cast() shinylive, need remove curl dependency. accomplish , shiny_deploy() helper functions moved package project.aid. realising REDCapR curl dependency, culprit. REDCapCAST going shinylive web-app without removing REDCapR dependency REDCap database interaction, defy purpose. ’ll stick hosted Shiny app instead.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2421","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.2.1","title":"REDCapCAST 24.2.1","text":"CRAN release: 2024-02-28","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-2-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.2.1","text":"Fix: ds2dd(): uses correct default dd column names. deprecated. Fix: easy_redcap(): fixed actually allow project naming. also specifically asks uri. widening updated work. Fix: redcap_wider(): updated accept formats allow handling simple projects without repeating instruments longitudinal. Fix: read_redcap_tables(): now handles non-longitudinal project without repeatable instruments. NEW: ds2dd_detailed(): extension ds2dd(), serves preserve much metadata possible automatically. Depends group helper functions also introduced. special note guess_time_only_filter(), try guess columns/variables formatted time formats. Supports hms time format. DETAILED INSTRUCTION VIGNETTE PENDING. NEW: read_redcap_instrument(): convenience function retrieve complete instrument. Goes little focused approach. REDCapR::redcap_read() can specify form download. also specify record id variable though. done read_redcap_instrument(). Nothing fancy. NEW: shiny_cast(): Shiny application ease process converting spreadsheet/data set REDCap database. app runs locally data transferred securely. can just create upload data dictionary, can also transfer given data process. plan host app shinyapps.io, now can run locally.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"other-24-2-1","dir":"Changelog","previous_headings":"","what":"Other","title":"REDCapCAST 24.2.1","text":"believe renv now added runs correctly. clone, renv::restore() install necessary package modify package. seems always back forth. renv may way . Added Code Conduct.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2411","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.1.1","title":"REDCapCAST 24.1.1","text":"CRAN release: 2024-01-09","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-1-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.1.1","text":"Fix: read_redcap_tables(): checking form names based data dictionary allow handling non-longitudinal projects. Prints invalid form names invalid event names. invalid form names supplied REDCapR::redcap_read() (backbone), forms exported, want focused approach. Invalid event names give output rather peculiar formatting. Checking field names validity also added.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-23121","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.12.1","title":"REDCapCAST 23.12.1","text":"CRAN release: 2023-12-20 One new function ease secure dataset retrieval bug fixes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-12-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.12.1","text":"New: easy_redcap() function ease retrieval dataset read_redcap_tables() keyring-package based key storage, handles secure API set, storage retrieval. Relies small helper function, get_api_key(), wraps relevant keyring-functions. Includes option cast data wide format flag widen.data. Fix: REDCap_split(): using function , supplying data set check boxes fail metadata supplied tibble. Metadata now converted data.frame. Fixed. Fix: read_redcap_tables(): fixed bug supplying events.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2362","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.2","title":"REDCapCAST 23.6.2","text":"CRAN release: 2023-07-04 version marks introduction helper functions handle database creation.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-6-2","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.6.2","text":"New: ds2dd() function migrating stRoke-package. Assists building data dictionary REDCap dataset. New: strsplitx() function ease string splitting extension base::strsplit(). Inspiration https://stackoverflow.com//11014253/21019325 https://www.r-bloggers.com/2018/04/strsplit--keeping--delimiter/. New: d2n() function converts single digits written numbers. Used sanitize variable form names REDCap database creation. universal number word suggest english::word() xfun::numbers_to_words(), though testing .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2361","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.1","title":"REDCapCAST 23.6.1","text":"CRAN release: 2023-06-06","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-6-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.6.1","text":"Updated description. Look! hex icon! Heading CRAN.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-4-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.4.1","text":"Aiming CRAN","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-3-2","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.3.2","text":"Page added. Vignettes follow. GithubActions tests added code coverage assessed. Badge galore..","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"new-name-redcapcast-23-3-1","dir":"Changelog","previous_headings":"","what":"New name: REDCapCAST","title":"REDCapCAST 23.3.1","text":"reflect new functions limitation working R, changed naming fork, still, course, maintaining status fork. versioning moved monthly naming convention. main goal package keep option export defined subset whole dataset REDCap server made possible REDCapR::redcap_read() function, combine work put REDCapRITS package handling longitudinal projects /projects repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-3-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 23.3.1","text":"read_redcap_tables() NEW: function mainly implementation combined use REDCapR::readcap_read() REDCap_split() maintain focused nature REDCapR::readcap_read(), download specified data. Also implements tests valid form names event names. usual fall-back solution get data. redcap_wider() NEW: function pivots long data frames read_redcap_tables() using tidyr::pivot_wider(). focused_metadata() NEW: hidden helper function enable focused data acquisition approach handle subset metadata corresponding focused dataset.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"notes-23-3-1","dir":"Changelog","previous_headings":"","what":"Notes:","title":"REDCapCAST 23.3.1","text":"metadata handling IMPROVED: improved handling different column names matadata (DataDictionary) REDCap dependent whether acquired thorugh api og downloaded server.","code":""}]
+[{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement andreas@gdamsbo.dk. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. 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Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Automatic Licensing of Downstream Recipients","title":"GNU General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. 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Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"two-different-ways-to-create-a-data-base","dir":"Articles","previous_headings":"","what":"Two different ways to create a data base","title":"Database-creation","text":"REDCapCAST provides two approaches creating data dictionary aimed helping two different cases: Easily create REDCap data base existing data set. Create table Word describing variables data base use create data base. following try come suggestions use approaches.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"easy-data-set-to-data-base-workflow","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Easy data set to data base workflow","title":"Database-creation","text":"first iteration dataset data dictionary function ds2dd(), creates basic data dictionary variables stored text. sufficient just storing old datasets/spreadsheets securely REDCap. advanced ds2dd_detailed() natural development. try apply common data classes data validation assume first column id number. outputs list dataset modified variable names comply REDCap naming conventions data dictionary. dataset correctly formatted data dictionary preserve much information possible. Additional specifications DataDictionary can made manually, can uploaded modified manually graphical user interface REDCap server.","code":"d1 <- mtcars |>   dplyr::mutate(record_id = seq_len(dplyr::n())) |>   ds2dd()   d1 |>   gt::gt() d2 <- REDCapCAST::redcapcast_data |>    dplyr::mutate(record_id = seq_len(dplyr::n()),                 region=factor(region)) |>   dplyr::select(record_id, dplyr::everything()) |>   (\\(.x){     .x[!grepl(\"_complete$\",names(.x))]   })() |>    (\\(.x){     .x[!grepl(\"^redcap\",names(.x))]   })() |>     ds2dd_detailed() |>    purrr::pluck(\"meta\")   d2 |>    gt::gt()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"data-base-from-table","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Data base from table","title":"Database-creation","text":"…instructions examples coming…","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"meta-data-and-data-upload","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Meta data and data upload","title":"Database-creation","text":"Now DataDictionary can exported spreadsheet uploaded can uploaded using REDCapR package (projects “Development” status). Use one two approaches :","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"manual-upload","dir":"Articles","previous_headings":"Two different ways to create a data base > Meta data and data upload","what":"Manual upload","title":"Database-creation","text":"","code":"write.csv(dd_ls$meta, \"datadictionary.csv\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"upload-with-redcapr","dir":"Articles","previous_headings":"Two different ways to create a data base > Meta data and data upload","what":"Upload with REDCapR","title":"Database-creation","text":"“REDCap R Handbook” written interfacing REDCap R using library(keyring)store credentials chapter 1.1.","code":"REDCapR::redcap_metadata_write(   dd_ls$meta,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-4---data-upload","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Step 4 - Data upload","title":"Database-creation","text":"two options available data upload meta data upload: manual REDCapR. latter shown .","code":"REDCapR::redcap_write(   dd_ls$data,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"splitting-the-dataset","dir":"Articles","previous_headings":"","what":"Splitting the dataset","title":"REDCapCAST","text":"","code":"redcapcast_data |> gt::gt() redcapcast_meta |> gt::gt() list <-   REDCap_split(     records = redcapcast_data,     metadata = redcapcast_meta,     forms = \"all\"   ) |>    sanitize_split() str(list) #> List of 4 #>  $ baseline_data_start: tibble [6 × 14] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id                   : num [1:6] 1 2 3 4 5 6 #>   ..$ redcap_event_name           : chr [1:6] \"inclusion\" \"inclusion\" \"inclusion\" \"inclusion\" ... #>   ..$ cpr                         : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>   ..$ inclusion                   : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #>   ..$ inclusion_time              : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ... #>   .. ..- attr(*, \"units\")= chr \"secs\" #>   ..$ dob                         : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #>   ..$ age                         : num [1:6] 83 89.1 66.1 117.9 126.2 ... #>   ..$ age_integer                 : num [1:6] 83 89 66 117 126 91 #>   ..$ sex                         : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #>   ..$ cohabitation                : chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #>   ..$ hypertension                : chr [1:6] \"No\" \"No\" \"Yes\" NA ... #>   ..$ diabetes                    : chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #>   ..$ region                      : chr [1:6] \"East\" \"South\" \"North\" NA ... #>   ..$ baseline_data_start_complete: chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>   ..- attr(*, \"problems\")=<externalptr>  #>  $ mrs                : tibble [5 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id        : num [1:5] 1 2 2 3 3 #>   ..$ redcap_event_name: chr [1:5] \"inclusion\" \"inclusion\" \"follow1\" \"follow1\" ... #>   ..$ mrs_assessed     : chr [1:5] \"Yes\" \"Yes\" \"Yes\" \"Yes\" ... #>   ..$ mrs_date         : Date[1:5], format: \"2023-03-13\" \"2023-03-07\" ... #>   ..$ mrs_score        : num [1:5] 1 1 3 2 1 #>   ..$ mrs_complete     : chr [1:5] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>   ..- attr(*, \"problems\")=<externalptr>  #>  $ consensus          : tibble [0 × 5] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id         : num(0)  #>   ..$ redcap_event_name : chr(0)  #>   ..$ con_mrs           : logi(0)  #>   ..$ con_calc          : logi(0)  #>   ..$ consensus_complete: chr(0)  #>   ..- attr(*, \"problems\")=<externalptr>  #>  $ new_event          : tibble [13 × 8] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id               : num [1:13] 2 3 3 3 3 3 4 4 4 4 ... #>   ..$ redcap_event_name       : chr [1:13] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #>   ..$ redcap_repeat_instrument: chr [1:13] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #>   ..$ redcap_repeat_instance  : num [1:13] 1 1 2 1 2 3 1 2 1 2 ... #>   ..$ event_datetime          : POSIXct[1:13], format: \"2024-01-18 12:49:42\" \"2024-01-18 12:49:58\" ... #>   ..$ event_age               : num [1:13] NA NA NA NA NA NA 96 105 118 118 ... #>   ..$ event_type              : chr [1:13] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #>   ..$ new_event_complete      : chr [1:13] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>   ..- attr(*, \"problems\")=<externalptr>"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"reading-data-from-redcap","dir":"Articles","previous_headings":"","what":"Reading data from REDCap","title":"REDCapCAST","text":"function wraps demonstrated function get dataset, metadata, apply REDCap_splitfunction bit cleaning. just cuts outs steps easier approach. function works similar REDCapR::redcap_read() allowing specify fields, events forms export instead exporting whole database filtering afterwards. believe better safer, focused approach.","code":"# read_redcap_tables(uri = \"YOUR URI\", token = \"YOUR TOKEN\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"pivotting-to-wider-format","dir":"Articles","previous_headings":"","what":"Pivotting to wider format","title":"REDCapCAST","text":"","code":"redcap_wider(list) |> str() #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> 'data.frame':    6 obs. of  52 variables: #>  $ record_id                   : num  1 2 3 4 5 6 #>  $ cpr                         : chr  \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>  $ inclusion                   : Date, format: \"2023-03-13\" \"2023-03-01\" ... #>  $ inclusion_time              : 'hms' num  12:38:49 10:38:57 12:01:07 20:39:19 ... #>   ..- attr(*, \"units\")= chr \"secs\" #>  $ dob                         : Date, format: \"1940-03-12\" \"1934-02-01\" ... #>  $ age                         : num  83 89.1 66.1 117.9 126.2 ... #>  $ age_integer                 : num  83 89 66 117 126 91 #>  $ sex                         : chr  \"female\" \"male\" \"male\" \"female\" ... #>  $ cohabitation                : chr  \"Yes\" \"Yes\" \"No\" NA ... #>  $ hypertension                : chr  \"No\" \"No\" \"Yes\" NA ... #>  $ diabetes                    : chr  \"Yes\" \"No\" \"Yes\" NA ... #>  $ region                      : chr  \"East\" \"South\" \"North\" NA ... #>  $ baseline_data_start_complete: chr  \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ mrs_assessed_inclusion      : chr  \"Yes\" \"Yes\" NA NA ... #>  $ mrs_assessed_follow1        : chr  NA \"Yes\" \"Yes\" NA ... #>  $ mrs_assessed_follow2        : chr  NA NA \"Yes\" NA ... #>  $ mrs_date_inclusion          : Date, format: \"2023-03-13\" \"2023-03-07\" ... #>  $ mrs_date_follow1            : Date, format: NA \"2023-03-09\" ... #>  $ mrs_date_follow2            : Date, format: NA NA ... #>  $ mrs_score_inclusion         : num  1 1 NA NA NA NA #>  $ mrs_score_follow1           : num  NA 3 2 NA NA NA #>  $ mrs_score_follow2           : num  NA NA 1 NA NA NA #>  $ mrs_complete_inclusion      : chr  \"Incomplete\" \"Incomplete\" NA NA ... #>  $ mrs_complete_follow1        : chr  NA \"Incomplete\" \"Incomplete\" NA ... #>  $ mrs_complete_follow2        : chr  NA NA \"Incomplete\" NA ... #>  $ con_mrs                     : logi  NA NA NA NA NA NA #>  $ con_calc                    : logi  NA NA NA NA NA NA #>  $ consensus_complete          : chr  NA NA NA NA ... #>  $ event_datetime_1_follow1    : POSIXct, format: NA \"2024-01-18 12:49:42\" ... #>  $ event_datetime_1_follow2    : POSIXct, format: NA NA ... #>  $ event_age_1_follow1         : num  NA NA NA 96 127 NA #>  $ event_age_1_follow2         : num  NA NA NA 118 NA NA #>  $ event_type_1_follow1        : chr  NA \"TIA\" \"AIS\" \"TIA\" ... #>  $ event_type_1_follow2        : chr  NA NA \"ICH\" \"AIS\" ... #>  $ new_event_complete_1_follow1: chr  NA \"Incomplete\" \"Incomplete\" \"Complete\" ... #>  $ new_event_complete_1_follow2: chr  NA NA \"Incomplete\" \"Complete\" ... #>  $ event_datetime_2_follow1    : POSIXct, format: NA NA ... #>  $ event_datetime_2_follow2    : POSIXct, format: NA NA ... #>  $ event_datetime_3_follow1    : POSIXct, format: NA NA ... #>  $ event_datetime_3_follow2    : POSIXct, format: NA NA ... #>  $ event_age_2_follow1         : num  NA NA NA 105 127 NA #>  $ event_age_2_follow2         : num  NA NA NA 118 NA NA #>  $ event_age_3_follow1         : num  NA NA NA NA NA NA #>  $ event_age_3_follow2         : num  NA NA NA 118 NA NA #>  $ event_type_2_follow1        : chr  NA NA \"ICH\" \"TIA\" ... #>  $ event_type_2_follow2        : chr  NA NA \"TIA\" \"ICH\" ... #>  $ event_type_3_follow1        : chr  NA NA NA NA ... #>  $ event_type_3_follow2        : chr  NA NA \"AIS\" \"Unknown\" ... #>  $ new_event_complete_2_follow1: chr  NA NA \"Incomplete\" \"Complete\" ... #>  $ new_event_complete_2_follow2: chr  NA NA \"Incomplete\" \"Incomplete\" ... #>  $ new_event_complete_3_follow1: chr  NA NA NA NA ... #>  $ new_event_complete_3_follow2: chr  NA NA \"Incomplete\" \"Complete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer. Paul Egeler. Author.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo , Egeler P (2024). REDCapCAST: REDCap Metadata Casting Castellated Data Handling. R package version 24.11.4, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{,   title = {REDCapCAST: REDCap Metadata Casting and Castellated Data Handling},   author = {Andreas Gammelgaard Damsbo and Paul Egeler},   year = {2024},   note = {R package version 24.11.4, https://agdamsbo.github.io/REDCapCAST/},   url = {https://github.com/agdamsbo/REDCapCAST}, }"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"redcapcast-package-","dir":"","previous_headings":"","what":"REDCap Metadata Casting and Castellated Data Handling","title":"REDCap Metadata Casting and Castellated Data Handling","text":"Casting metadata REDCap database creation handling castellated data using repeated instruments longitudinal projects REDCap. implemented app-interface easy database creation accessible available run locally shiny_cast() allowing easily create REDCap database based existing spreadsheet. Export data REDCap different formats handling castellated data, default export requested data, mainly read_redcap_tables(). REDCapCAST initially build , still includes code pegeler/REDCapRITS, relies functions REDCapR-project","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"history","dir":"","previous_headings":"","what":"History","title":"REDCap Metadata Casting and Castellated Data Handling","text":"package originally forked pegeler/REDCapRITS. REDCapRITS represents great extensive work handle castellated REDCap data different programming languages. REDCapCAST evolved much just handling castellated data detatched original project still relying main REDCap_split function. access REDCap database build outstanding work REDCapR. package really started frustration PhD health science hearing colleagues complaining “castellated” data formatting REDCap exports longitudinal projects used wide data. led bad decisions building databases avoiding repeated instruments. package solves challenges, solutions also implemented else like redcapAPI REDCapTidieR packages, bigger project. help new PhD students researchers, also worked creating helper/wrapper-functions ease data access. Documentation ’s way. advanced uses, consider using redcapAPI REDCapR packages.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"REDCap Metadata Casting and Castellated Data Handling","text":"plan package bundled Handbook working REDCap R. work progress limited time available. Please feel free contact create issue ideas future additions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"installation-and-use","dir":"","previous_headings":"","what":"Installation and use","title":"REDCap Metadata Casting and Castellated Data Handling","text":"package available CRAN. Install latest version: Install latest version directly GitHub: Launch REDCapCAST app interface directly machine:","code":"install.packages(\"REDCapCAST\") require(\"remotes\") remotes::install_github(\"agdamsbo/REDCapCAST\") REDCapCAST::shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"REDCap Metadata Casting and Castellated Data Handling","text":"Please note REDCapCAST project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCapCAST-package.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","title":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","text":"Casting metadata REDCap database creation handling castellated data using repeated instruments longitudinal projects 'REDCap'. Keeps focused data export approach, allowing export required data database. Also casting new REDCap databases based datasets sources. Originally forked R part 'REDCapRITS' Paul Egeler. See https://github.com/pegeler/REDCapRITS. 'REDCap' (Research Electronic Data Capture) secure, web-based software platform designed support data capture research studies, providing 1) intuitive interface validated data capture; 2) audit trails tracking data manipulation export procedures; 3) automated export procedures seamless data downloads common statistical packages; 4) procedures data integration interoperability external sources (Harris et al (2009) doi:10.1016/j.jbi.2008.08.010 ; Harris et al (2019) doi:10.1016/j.jbi.2019.103208 ).","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCapCAST-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","text":"Maintainer: Andreas Gammelgaard Damsbo agdamsbo@clin.au.dk (ORCID) Authors: Paul Egeler paulegeler@gmail.com (ORCID)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split REDCap repeating instruments table into multiple tables — REDCap_split","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"take output REDCap export split base table child tables repeating instrument. Metadata used determine fields included resultant table.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"REDCap_split(   records,   metadata,   primary_table_name = \"\",   forms = c(\"repeating\", \"all\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"records Exported project records. May data.frame, response, character vector containing JSON API call. metadata Project metadata (data dictionary). May data.frame, response, character vector containing JSON API call. primary_table_name Name given list element primary output table (described README.md). Ignored forms = ''. forms Indicate whether create separate tables repeating instruments forms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"list \"data.frame\"s. number tables differ   depending forms option selected. 'repeating': one base table one     tables repeating instrument. '': data.frame instrument, regardless     whether repeating instrument .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"Paul W. Egeler, M.S., GStat","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"if (FALSE) { # \\dontrun{ # Using an API call -------------------------------------------------------  library(RCurl)  # Get the records records <- postForm(   uri = api_url, # Supply your site-specific URI   token = api_token, # Supply your own API token   content = \"record\",   format = \"json\",   returnFormat = \"json\" )  # Get the metadata metadata <- postForm(   uri = api_url, # Supply your site-specific URI   token = api_token, # Supply your own API token   content = \"metadata\",   format = \"json\" )  # Convert exported JSON strings into a list of data.frames REDCapRITS::REDCap_split(records, metadata)  # Using a raw data export -------------------------------------------------  # Get the records records <- read.csv(\"/path/to/data/ExampleProject_DATA_2018-06-03_1700.csv\")  # Get the metadata metadata <- read.csv(   \"/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv\" )  # Split the tables REDCapRITS::REDCap_split(records, metadata)  # In conjunction with the R export script ---------------------------------  # You must set the working directory first since the REDCap data export # script contains relative file references. old <- getwd() setwd(\"/path/to/data/\")  # Run the data export script supplied by REDCap. # This will create a data.frame of your records called 'data' source(\"ExampleProject_R_2018-06-03_1700.r\")  # Get the metadatan metadata <- read.csv(\"ExampleProject_DataDictionary_2018-06-03.csv\")  # Split the tables REDCapRITS::REDCap_split(data, metadata) setwd(old) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if vector is all NA — all_na","title":"Check if vector is all NA — all_na","text":"Check vector NA","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if vector is all NA — all_na","text":"","code":"all_na(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if vector is all NA — all_na","text":"data vector data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if vector is all NA — all_na","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if vector is all NA — all_na","text":"","code":"rep(NA, 4) |> all_na() #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"Preserve factor levels REDCap data dictionary data export","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"","code":"apply_factor_labels(data, meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"data REDCap exported data set meta REDCap data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply REDCap filed labels to data frame — apply_field_label","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"Apply REDCap filed labels data frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"","code":"apply_field_label(data, meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"data REDCap exported data set meta REDCap data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert labelled vectors to factors while preserving attributes — as_factor","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"extends [forcats::as_factor()] well [haven::as_factor()], appending original attributes except \"class\" converting factor avoid ta loss case rich formatted labelled data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"","code":"as_factor(x, ...)  # S3 method for class 'factor' as_factor(x, ...)  # S3 method for class 'logical' as_factor(x, ...)  # S3 method for class 'numeric' as_factor(x, ...)  # S3 method for class 'character' as_factor(x, ...)  # S3 method for class 'haven_labelled' as_factor(   x,   levels = c(\"default\", \"labels\", \"values\", \"both\"),   ordered = FALSE,   ... )  # S3 method for class 'labelled' as_factor(   x,   levels = c(\"default\", \"labels\", \"values\", \"both\"),   ordered = FALSE,   ... )  # S3 method for class 'redcapcast_labelled' as_factor(   x,   levels = c(\"default\", \"labels\", \"values\", \"both\"),   ordered = FALSE,   ... )  # S3 method for class 'data.frame' as_factor(x, ..., only_labelled = TRUE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"x Object coerce factor. ... arguments passed method. levels create levels generated factor: * \"default\": uses labels available, otherwise values.     Labels sorted value.   * \"\": like \"default\", pastes together level value   * \"label\": use labels; unlabelled values become `NA`   * \"values\": use values ordered `TRUE` create ordered (ordinal) factor, `FALSE` (default) create regular (nominal) factor. only_labelled apply labelled columns?","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"Please refer parent functions extended documentation. avoid redundancy calls errors, functions copy-pasted ","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"","code":"# will preserve all attributes c(1, 4, 3, \"A\", 7, 8, 1) |> as_factor() #> Warning: invalid roman numeral: A #> [1] 1 4 3 A 7 8 1 #> Levels: 1 4 3 A 7 8 structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10) ) |>   as_factor() |>   dput() #> structure(c(1L, 2L, 3L, 2L, 5L, 4L), levels = c(\"1\", \"2\", \"3\",  #> \"9\", \"10\"), class = \"factor\", labels = c(Unknown = 9, Refused = 10 #> ))  structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |>   as_factor() #> [1] 1       2       3       2       Refused Unknown #> attr(,\"labels\") #> Unknown Refused  #>       9      10  #> Levels: 1 2 3 Unknown Refused"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List-base regex case_when — case_match_regex_list","title":"List-base regex case_when — case_match_regex_list","text":"Mimics case_when list regex patterns values. Used date/time validation generation name vector. Like case_when, matches order priority. Primarily used REDCapCAST data type coding systematic variable naming.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List-base regex case_when — case_match_regex_list","text":"","code":"case_match_regex_list(data, match.list, .default = NA)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List-base regex case_when — case_match_regex_list","text":"data vector match.list list case matches .default Default value non-matches. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List-base regex case_when — case_match_regex_list","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List-base regex case_when — case_match_regex_list","text":"","code":"case_match_regex_list(   c(\"test_date\", \"test_time\", \"test_tida\", \"test_tid\"),   list(date_dmy = \"_dat[eo]$\", time_hh_mm_ss = \"_ti[md]e?$\") ) #> [1] \"date_dmy\"      \"time_hh_mm_ss\" NA              \"time_hh_mm_ss\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":null,"dir":"Reference","previous_headings":"","what":"Overview of REDCapCAST data for shiny — cast_data_overview","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"Overview REDCapCAST data shiny","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"","code":"cast_data_overview(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"data list class 'REDCapCAST'","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"gt object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":null,"dir":"Reference","previous_headings":"","what":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"Overview REDCapCAST meta data shiny","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"","code":"cast_meta_overview(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"data list class 'REDCapCAST'","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"gt object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple function to generate REDCap choices from character vector — char2choice","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"Simple function generate REDCap choices character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"","code":"char2choice(data, char.split = \"/\", raw = NULL, .default = NA)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"data vector char.split splitting character(s) raw specific values. Can used options length. .default default value missing. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"","code":"char2choice(c(\"yes/no\",\"  yep. / nope  \",\"\",NA,\"what\"),.default=NA) #> [1] \"1, yes | 2, no\"    \"1, yep. | 2, nope\" NA                  #> [4] NA                  \"1, what\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple function to generate REDCap branching logic from character vector — char2cond","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"Simple function generate REDCap branching logic character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"","code":"char2cond(   data,   minor.split = \",\",   major.split = \";\",   major.sep = \" or \",   .default = NA )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"data vector minor.split minor split major.split major split major.sep argument separation. Default \" \". .default default value missing. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"","code":"#data <- dd_inst$betingelse #c(\"Extubation_novent, 2; Pacu_delay, 1\") |> char2cond()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"simple function remove rich text formatting field label save first paragraph ('<p>...<\/p>').","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"","code":"clean_field_label(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"data field label","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('<p>...<\/p>'). — clean_field_label","text":"","code":"clean_field_label(\"<div class=\\\"rich-text-field-label\\\"><p>Fazekas score<\/p><\/div>\") #> [1] \"Fazekas score\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":null,"dir":"Reference","previous_headings":"","what":"clean_redcap_name — clean_redcap_name","title":"clean_redcap_name — clean_redcap_name","text":"Stepwise removal non-alphanumeric characters, trailing white space, substitutes spaces underscores converts lower case. Trying make different naming conventions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clean_redcap_name — clean_redcap_name","text":"","code":"clean_redcap_name(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clean_redcap_name — clean_redcap_name","text":"x vector data frame cleaning","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clean_redcap_name — clean_redcap_name","text":"vector data frame, format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Compacting a vector of any length with or without names — compact_vec","title":"Compacting a vector of any length with or without names — compact_vec","text":"Compacting vector length without names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compacting a vector of any length with or without names — compact_vec","text":"","code":"compact_vec(data, nm.sep = \": \", val.sep = \"; \")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compacting a vector of any length with or without names — compact_vec","text":"data vector, optionally named nm.sep string separating name value val.sep string separating values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compacting a vector of any length with or without names — compact_vec","text":"character string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/compact_vec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compacting a vector of any length with or without names — compact_vec","text":"","code":"sample(seq_len(4), 20, TRUE) |>   as_factor() |>   named_levels() |>   sort() |>   compact_vec() #> [1] \"1: 1; 2: 2; 3: 3; 4: 4\" 1:6 |> compact_vec() #> [1] \"1; 2; 3; 4; 5; 6\" \"test\" |> compact_vec() #> [1] \"test\" sample(letters[1:9], 20, TRUE) |> compact_vec() #> [1] \"g; e; e; b; f; d; b; c; i; f; g; e; f; i; f; e; b; a; d; h\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"Create two-column HTML table data piping REDCap instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"","code":"create_html_table(text, variable)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"text descriptive text variable variable pipe","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_html_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create two-column HTML table for data piping in REDCap instruments — create_html_table","text":"","code":"create_html_table(text = \"Patient ID\", variable = c(\"[cpr]\")) #> <table style=\"border-collapse: collapse; width: 100%;\" border=\"0\"> <tbody><tr> <td style=\"width: 58%;\"> <h5><span style=\"font-weight: normal;\">Patient ID<br /><\/span><\/h5> <\/td> <td style=\"width: 42%; text-align: left;\"> <h5><span style=\"font-weight: bold;\">[cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> create_html_table(text = paste(\"assessor\", 1:2, sep = \"_\"), variable = c(\"[cpr]\")) #> <table style=\"border-collapse: collapse; width: 100%;\" border=\"0\"> <tbody><tr> <td style=\"width: 58%;\"> <h5><span style=\"font-weight: normal;\">assessor_1<br /><\/span><\/h5> <\/td> <td style=\"width: 42%; text-align: left;\"> <h5><span style=\"font-weight: bold;\">[cpr]<\/span><\/h5> <\/td> <\/tr><tr> <td style=\"width: 58%;\"> <h5><span style=\"font-weight: normal;\">assessor_2<br /><\/span><\/h5> <\/td> <td style=\"width: 42%; text-align: left;\"> <h5><span style=\"font-weight: bold;\">[cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> # create_html_table(text = c(\"CPR nummer\",\"Word\"), variable = c(\"[cpr][1]\", \"[cpr][2]\", \"[test]\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"Metadata can added editing data dictionary project initial design phase. want later add new instruments, function can used create () instrument(s) add project production.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"","code":"create_instrument_meta(data, dir = here::here(\"\"), record.id = TRUE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"data metadata relevant instrument. `ds2dd_detailed()` dir destination dir instrument zip. Default current WD. record.id flag omit first row data dictionary assuming record_id field included instrument. Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"","code":"if (FALSE) { # \\dontrun{ data <- iris |>   ds2dd_detailed(     add.auto.id = TRUE,     form.name = sample(c(\"b\", \"c\"),       size = 6,       replace = TRUE, prob = rep(.5, 2)     )   ) |>   purrr::pluck(\"meta\") # data |> create_instrument_meta()  data <- iris |>   ds2dd_detailed(add.auto.id = FALSE) |>   purrr::pluck(\"data\") iris |>   setNames(glue::glue(\"{sample(x = c('a','b'),size = length(ncol(iris)), replace=TRUE,prob = rep(x=.5,2))}__{names(iris)}\")) |>   ds2dd_detailed(form.sep = \"__\") data |>   purrr::pluck(\"meta\") |>   create_instrument_meta(record.id = FALSE) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert single digits to words — d2w","title":"Convert single digits to words — d2w","text":"Convert single digits words","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert single digits to words — d2w","text":"","code":"d2w(x, lang = \"en\", neutrum = FALSE, everything = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert single digits to words — d2w","text":"x data. Handle vectors, data.frames lists lang language. Danish (da) English (en), Default \"en\" neutrum numbers depending counted word everything flag also split numbers >9 single digits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert single digits to words — d2w","text":"returns characters format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert single digits to words — d2w","text":"","code":"d2w(c(2:8, 21)) #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" \"21\"    d2w(data.frame(2:7, 3:8, 1), lang = \"da\", neutrum = TRUE) #>   X2.7 X3.8 X1 #> 1   to  tre et #> 2  tre fire et #> 3 fire  fem et #> 4  fem seks et #> 5 seks  syv et #> 6  syv otte et  ## If everything=T, also larger numbers are reduced. ## Elements in the list are same length as input d2w(list(2:8, c(2, 6, 4, 23), 2), everything = TRUE) #> [[1]] #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" #>  #> [[2]] #> [1] \"two\"       \"six\"       \"four\"      \"two three\" #>  #> [[3]] #> [1] \"two\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"Works well `project.aid::docx2list()`. Allows defining database text document (see provided template) easier use data base creation. approach allows easier collaboration defining database. generic case data frame variable names values column. format like REDCap data dictionary, gives options formatting.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"","code":"doc2dd(   data,   instrument.name,   col.variables = 1,   list.datetime.format = list(date_dmy = \"_dat[eo]$\", time_hh_mm_ss = \"_ti[md]e?$\"),   col.description = NULL,   col.condition = NULL,   col.subheader = NULL,   subheader.tag = \"h2\",   condition.minor.sep = \",\",   condition.major.sep = \";\",   col.calculation = NULL,   col.choices = NULL,   choices.char.sep = \"/\",   missing.default = NA )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"data tibble data.frame variable names one column instrument.name character vector length one. Instrument name. col.variables variable names column (default = 1), allows dplyr subsetting list.datetime.format formatting date/time detection. See `case_match_regex_list()` col.description descriptions column, allows dplyr subsetting. empty, variable names used. col.condition conditions branching column, allows dplyr subsetting. See `char2cond()`. col.subheader sub-header column, allows dplyr subsetting. See `format_subheader()`. subheader.tag formatting tag. Default \"h2\" condition.minor.sep condition split minor. See `char2cond()`. Default \",\". condition.major.sep condition split major. See `char2cond()`. Default \";\". col.calculation calculations column. written exact. Character vector. col.choices choices column. See `char2choice()`. choices.char.sep choices split. See `char2choice()`. Default \"/\". missing.default value missing fields. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"tibble data.frame (data)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"","code":"# data <- dd_inst # data |> doc2dd(instrument.name = \"evt\", # col.description = 3, # col.condition = 4, # col.subheader = 2, # col.calculation = 5, # col.choices = 6)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"(DEPRECATED) Data set to data dictionary function — ds2dd","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Creates basic data dictionary skeleton. Please see `ds2dd_detailed()` advanced function.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"ds2dd(   ds,   record.id = \"record_id\",   form.name = \"basis\",   field.type = \"text\",   field.label = NULL,   include.column.names = FALSE,   metadata = names(REDCapCAST::redcapcast_meta) )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"ds data set record.id name column number id variable, moved first row data dictionary, character integer. Default \"record_id\". form.name vector form names, character string, length 1 length equal number variables. Default \"basis\". field.type vector field types, character string, length 1 length equal number variables. Default \"text. field.label vector form names, character string, length 1 length equal number variables. Default NULL identical field names. include.column.names Flag give detailed output including new column names original data set upload. metadata Metadata column names. Default included names(REDCapCAST::redcapcast_meta).","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"data.frame list data.frame vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Migrated stRoke ds2dd(). Fits better functionality 'REDCapCAST'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"redcapcast_data$record_id <- seq_len(nrow(redcapcast_data)) ds2dd(redcapcast_data, include.column.names=TRUE) #> $DataDictionary #>                      field_name form_name section_header field_type #> 1                     record_id     basis             NA       text #> 2             redcap_event_name     basis             NA       text #> 3      redcap_repeat_instrument     basis             NA       text #> 4        redcap_repeat_instance     basis             NA       text #> 5                           cpr     basis             NA       text #> 6                     inclusion     basis             NA       text #> 7                inclusion_time     basis             NA       text #> 8                           dob     basis             NA       text #> 9                           age     basis             NA       text #> 10                  age_integer     basis             NA       text #> 11                          sex     basis             NA       text #> 12                 cohabitation     basis             NA       text #> 13                 hypertension     basis             NA       text #> 14                     diabetes     basis             NA       text #> 15                       region     basis             NA       text #> 16 baseline_data_start_complete     basis             NA       text #> 17                 mrs_assessed     basis             NA       text #> 18                     mrs_date     basis             NA       text #> 19                    mrs_score     basis             NA       text #> 20                 mrs_complete     basis             NA       text #> 21                      con_mrs     basis             NA       text #> 22                     con_calc     basis             NA       text #> 23           consensus_complete     basis             NA       text #> 24               event_datetime     basis             NA       text #> 25                    event_age     basis             NA       text #> 26                   event_type     basis             NA       text #> 27           new_event_complete     basis             NA       text #>                     field_label select_choices_or_calculations field_note #> 1                     record_id                             NA         NA #> 2             redcap_event_name                             NA         NA #> 3      redcap_repeat_instrument                             NA         NA #> 4        redcap_repeat_instance                             NA         NA #> 5                           cpr                             NA         NA #> 6                     inclusion                             NA         NA #> 7                inclusion_time                             NA         NA #> 8                           dob                             NA         NA #> 9                           age                             NA         NA #> 10                  age_integer                             NA         NA #> 11                          sex                             NA         NA #> 12                 cohabitation                             NA         NA #> 13                 hypertension                             NA         NA #> 14                     diabetes                             NA         NA #> 15                       region                             NA         NA #> 16 baseline_data_start_complete                             NA         NA #> 17                 mrs_assessed                             NA         NA #> 18                     mrs_date                             NA         NA #> 19                    mrs_score                             NA         NA #> 20                 mrs_complete                             NA         NA #> 21                      con_mrs                             NA         NA #> 22                     con_calc                             NA         NA #> 23           consensus_complete                             NA         NA #> 24               event_datetime                             NA         NA #> 25                    event_age                             NA         NA #> 26                   event_type                             NA         NA #> 27           new_event_complete                             NA         NA #>    text_validation_type_or_show_slider_number text_validation_min #> 1                                          NA                  NA #> 2                                          NA                  NA #> 3                                          NA                  NA #> 4                                          NA                  NA #> 5                                          NA                  NA #> 6                                          NA                  NA #> 7                                          NA                  NA #> 8                                          NA                  NA #> 9                                          NA                  NA #> 10                                         NA                  NA #> 11                                         NA                  NA #> 12                                         NA                  NA #> 13                                         NA                  NA #> 14                                         NA                  NA #> 15                                         NA                  NA #> 16                                         NA                  NA #> 17                                         NA                  NA #> 18                                         NA                  NA #> 19                                         NA                  NA #> 20                                         NA                  NA #> 21                                         NA                  NA #> 22                                         NA                  NA #> 23                                         NA                  NA #> 24                                         NA                  NA #> 25                                         NA                  NA #> 26                                         NA                  NA #> 27                                         NA                  NA #>    text_validation_max identifier branching_logic required_field #> 1                   NA         NA              NA             NA #> 2                   NA         NA              NA             NA #> 3                   NA         NA              NA             NA #> 4                   NA         NA              NA             NA #> 5                   NA         NA              NA             NA #> 6                   NA         NA              NA             NA #> 7                   NA         NA              NA             NA #> 8                   NA         NA              NA             NA #> 9                   NA         NA              NA             NA #> 10                  NA         NA              NA             NA #> 11                  NA         NA              NA             NA #> 12                  NA         NA              NA             NA #> 13                  NA         NA              NA             NA #> 14                  NA         NA              NA             NA #> 15                  NA         NA              NA             NA #> 16                  NA         NA              NA             NA #> 17                  NA         NA              NA             NA #> 18                  NA         NA              NA             NA #> 19                  NA         NA              NA             NA #> 20                  NA         NA              NA             NA #> 21                  NA         NA              NA             NA #> 22                  NA         NA              NA             NA #> 23                  NA         NA              NA             NA #> 24                  NA         NA              NA             NA #> 25                  NA         NA              NA             NA #> 26                  NA         NA              NA             NA #> 27                  NA         NA              NA             NA #>    custom_alignment question_number matrix_group_name matrix_ranking #> 1                NA              NA                NA             NA #> 2                NA              NA                NA             NA #> 3                NA              NA                NA             NA #> 4                NA              NA                NA             NA #> 5                NA              NA                NA             NA #> 6                NA              NA                NA             NA #> 7                NA              NA                NA             NA #> 8                NA              NA                NA             NA #> 9                NA              NA                NA             NA #> 10               NA              NA                NA             NA #> 11               NA              NA                NA             NA #> 12               NA              NA                NA             NA #> 13               NA              NA                NA             NA #> 14               NA              NA                NA             NA #> 15               NA              NA                NA             NA #> 16               NA              NA                NA             NA #> 17               NA              NA                NA             NA #> 18               NA              NA                NA             NA #> 19               NA              NA                NA             NA #> 20               NA              NA                NA             NA #> 21               NA              NA                NA             NA #> 22               NA              NA                NA             NA #> 23               NA              NA                NA             NA #> 24               NA              NA                NA             NA #> 25               NA              NA                NA             NA #> 26               NA              NA                NA             NA #> 27               NA              NA                NA             NA #>    field_annotation #> 1                NA #> 2                NA #> 3                NA #> 4                NA #> 5                NA #> 6                NA #> 7                NA #> 8                NA #> 9                NA #> 10               NA #> 11               NA #> 12               NA #> 13               NA #> 14               NA #> 15               NA #> 16               NA #> 17               NA #> 18               NA #> 19               NA #> 20               NA #> 21               NA #> 22               NA #> 23               NA #> 24               NA #> 25               NA #> 26               NA #> 27               NA #>  #> $`Column names` #>  [1] \"record_id\"                    \"redcap_event_name\"            #>  [3] \"redcap_repeat_instrument\"     \"redcap_repeat_instance\"       #>  [5] \"cpr\"                          \"inclusion\"                    #>  [7] \"inclusion_time\"               \"dob\"                          #>  [9] \"age\"                          \"age_integer\"                  #> [11] \"sex\"                          \"cohabitation\"                 #> [13] \"hypertension\"                 \"diabetes\"                     #> [15] \"region\"                       \"baseline_data_start_complete\" #> [17] \"mrs_assessed\"                 \"mrs_date\"                     #> [19] \"mrs_score\"                    \"mrs_complete\"                 #> [21] \"con_mrs\"                      \"con_calc\"                     #> [23] \"consensus_complete\"           \"event_datetime\"               #> [25] \"event_age\"                    \"event_type\"                   #> [27] \"new_event_complete\"           #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract data from stata file for data dictionary — ds2dd_detailed","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"Extract data stata file data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"ds2dd_detailed(   data,   add.auto.id = FALSE,   date.format = \"dmy\",   form.name = NULL,   form.sep = NULL,   form.prefix = TRUE,   field.type = NULL,   field.label = NULL,   field.label.attr = \"label\",   field.validation = NULL,   metadata = names(REDCapCAST::redcapcast_meta),   convert.logicals = TRUE )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"data data frame add.auto.id flag add id column date.format date format, character string. ymd/dmy/mdy. dafault dmy. form.name manually specify form name(s). Vector length 1 ncol(data). Default NULL \"data\" used. form.sep supplied dataset form names suffix prefix column/variable names, seperator can specified. supplied, form.name ignored. Default NULL. form.prefix Flag set form prefix (TRUE) suffix (FALSE) column names. Assumes columns pre- suffix specified. field.type manually specify field type(s). Vector length 1 ncol(data). Default NULL \"text\" used everything factors, wil get \"radio\". field.label manually specify field label(s). Vector length 1 ncol(data). Default NULL colnames(data) used attribute `field.label.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). field.label.attr attribute name named labels haven_labelled data set (imported .dta file `haven::read_dta()`. Default \"label\" field.validation manually specify field validation(s). Vector length 1 ncol(data). Default NULL `levels()` used factors attribute `factor.labels.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). metadata redcap metadata headings. Default names(REDCapCAST::redcapcast_meta). convert.logicals convert logicals factor. Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"list length 2","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"function natural development ds2dd() function. assumes first column ID-column. checks. Please, always inspect data dictionary upload. Ensure, data set formatted much information possible. `field.type` can supplied","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"## Basic parsing with default options requireNamespace(\"REDCapCAST\") redcapcast_data |>   dplyr::select(-dplyr::starts_with(\"redcap_\")) |>   ds2dd_detailed() #> $data #> # A tibble: 25 × 24 #>    record_id cpr    inclusion  inclusion_time dob          age age_integer sex   #>        <dbl> <chr>  <date>     <chr>          <date>     <dbl>       <dbl> <chr> #>  1         1 12034… 2023-03-13 12:38:49       1940-03-12  83.0          83 fema… #>  2         2 01023… 2023-03-01 10:38:57       1934-02-01  89.1          89 male  #>  3         2 NA     NA         NA             NA          NA            NA NA    #>  4         2 NA     NA         NA             NA          NA            NA NA    #>  5         3 23015… 2022-03-08 12:01:07       1956-01-23  66.1          66 male  #>  6         3 NA     NA         NA             NA          NA            NA NA    #>  7         3 NA     NA         NA             NA          NA            NA NA    #>  8         3 NA     NA         NA             NA          NA            NA NA    #>  9         3 NA     NA         NA             NA          NA            NA NA    #> 10         3 NA     NA         NA             NA          NA            NA NA    #> # ℹ 15 more rows #> # ℹ 16 more variables: cohabitation <chr>, hypertension <chr>, diabetes <chr>, #> #   region <chr>, baseline_data_start_complete <chr>, mrs_assessed <chr>, #> #   mrs_date <date>, mrs_score <dbl>, mrs_complete <chr>, con_mrs <fct>, #> #   con_calc <fct>, consensus_complete <chr>, event_datetime <dttm>, #> #   event_age <dbl>, event_type <chr>, new_event_complete <chr> #>  #> $meta #> # A tibble: 24 × 18 #>    field_name     form_name section_header field_type field_label    #>    <chr>          <chr>     <lgl>          <chr>      <chr>          #>  1 record_id      data      NA             text       record_id      #>  2 cpr            data      NA             text       cpr            #>  3 inclusion      data      NA             text       inclusion      #>  4 inclusion_time data      NA             text       inclusion_time #>  5 dob            data      NA             text       dob            #>  6 age            data      NA             text       age            #>  7 age_integer    data      NA             text       age_integer    #>  8 sex            data      NA             text       sex            #>  9 cohabitation   data      NA             text       cohabitation   #> 10 hypertension   data      NA             text       hypertension   #> # ℹ 14 more rows #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\"        ## Adding a record_id field iris |> ds2dd_detailed(add.auto.id = TRUE) #> $data #> # A tibble: 150 × 6 #>    record_id sepal.length sepal.width petal.length petal.width species #>        <int>        <dbl>       <dbl>        <dbl>       <dbl> <fct>   #>  1         1          5.1         3.5          1.4         0.2 setosa  #>  2         2          4.9         3            1.4         0.2 setosa  #>  3         3          4.7         3.2          1.3         0.2 setosa  #>  4         4          4.6         3.1          1.5         0.2 setosa  #>  5         5          5           3.6          1.4         0.2 setosa  #>  6         6          5.4         3.9          1.7         0.4 setosa  #>  7         7          4.6         3.4          1.4         0.3 setosa  #>  8         8          5           3.4          1.5         0.2 setosa  #>  9         9          4.4         2.9          1.4         0.2 setosa  #> 10        10          4.9         3.1          1.5         0.1 setosa  #> # ℹ 140 more rows #>  #> $meta #> # A tibble: 6 × 18 #>   field_name   form_name section_header field_type field_label  #>   <chr>        <chr>     <lgl>          <chr>      <chr>        #> 1 record_id    data      NA             text       record_id    #> 2 sepal.length data      NA             text       Sepal.Length #> 3 sepal.width  data      NA             text       Sepal.Width  #> 4 petal.length data      NA             text       Petal.Length #> 5 petal.width  data      NA             text       Petal.Width  #> 6 species      data      NA             radio      Species      #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\"        ## Passing form name information to function iris |>   ds2dd_detailed(     add.auto.id = TRUE,     form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2))   ) |>   purrr::pluck(\"meta\") #> # A tibble: 6 × 18 #>   field_name   form_name section_header field_type field_label  #>   <chr>        <chr>     <lgl>          <chr>      <chr>        #> 1 record_id    b         NA             text       record_id    #> 2 sepal.length c         NA             text       Sepal.Length #> 3 sepal.width  b         NA             text       Sepal.Width  #> 4 petal.length c         NA             text       Petal.Length #> 5 petal.width  b         NA             text       Petal.Width  #> 6 species      c         NA             radio      Species      #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> mtcars |> ds2dd_detailed(add.auto.id = TRUE) #> $data #> # A tibble: 32 × 12 #>    record_id   mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb #>        <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1         1  21       6  160    110  3.9   2.62  16.5     0     1     4     4 #>  2         2  21       6  160    110  3.9   2.88  17.0     0     1     4     4 #>  3         3  22.8     4  108     93  3.85  2.32  18.6     1     1     4     1 #>  4         4  21.4     6  258    110  3.08  3.22  19.4     1     0     3     1 #>  5         5  18.7     8  360    175  3.15  3.44  17.0     0     0     3     2 #>  6         6  18.1     6  225    105  2.76  3.46  20.2     1     0     3     1 #>  7         7  14.3     8  360    245  3.21  3.57  15.8     0     0     3     4 #>  8         8  24.4     4  147.    62  3.69  3.19  20       1     0     4     2 #>  9         9  22.8     4  141.    95  3.92  3.15  22.9     1     0     4     2 #> 10        10  19.2     6  168.   123  3.92  3.44  18.3     1     0     4     4 #> # ℹ 22 more rows #>  #> $meta #> # A tibble: 12 × 18 #>    field_name form_name section_header field_type field_label #>    <chr>      <chr>     <lgl>          <chr>      <chr>       #>  1 record_id  data      NA             text       record_id   #>  2 mpg        data      NA             text       mpg         #>  3 cyl        data      NA             text       cyl         #>  4 disp       data      NA             text       disp        #>  5 hp         data      NA             text       hp          #>  6 drat       data      NA             text       drat        #>  7 wt         data      NA             text       wt          #>  8 qsec       data      NA             text       qsec        #>  9 vs         data      NA             text       vs          #> 10 am         data      NA             text       am          #> 11 gear       data      NA             text       gear        #> 12 carb       data      NA             text       carb        #> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\"        ## Using column name suffix to carry form name data <- iris |>   ds2dd_detailed(add.auto.id = TRUE) |>   purrr::pluck(\"data\") names(data) <- glue::glue(\"{sample(x = c('a','b'),size = length(names(data)), replace=TRUE,prob = rep(x=.5,2))}__{names(data)}\") data |> ds2dd_detailed(form.sep = \"__\") #> $data #> # A tibble: 150 × 6 #>    record_id sepal.length sepal.width petal.length petal.width species #>        <int>        <dbl>       <dbl>        <dbl>       <dbl> <fct>   #>  1         1          5.1         3.5          1.4         0.2 setosa  #>  2         2          4.9         3            1.4         0.2 setosa  #>  3         3          4.7         3.2          1.3         0.2 setosa  #>  4         4          4.6         3.1          1.5         0.2 setosa  #>  5         5          5           3.6          1.4         0.2 setosa  #>  6         6          5.4         3.9          1.7         0.4 setosa  #>  7         7          4.6         3.4          1.4         0.3 setosa  #>  8         8          5           3.4          1.5         0.2 setosa  #>  9         9          4.4         2.9          1.4         0.2 setosa  #> 10        10          4.9         3.1          1.5         0.1 setosa  #> # ℹ 140 more rows #>  #> $meta #> # A tibble: 6 × 18 #>   field_name   form_name section_header field_type field_label  #>   <chr>        <chr>     <lgl>          <chr>      <chr>        #> 1 record_id    b         NA             text       record_id    #> 2 sepal.length a         NA             text       sepal.length #> 3 sepal.width  b         NA             text       sepal.width  #> 4 petal.length a         NA             text       petal.length #> 5 petal.width  b         NA             text       petal.width  #> 6 species      a         NA             radio      species      #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"Secure API key storage and data acquisition in one — easy_redcap","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"Secure API key storage data acquisition one","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"","code":"easy_redcap(project.name, widen.data = TRUE, uri, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"project.name name current project (key storage `keyring::key_set()`, using default keyring) widen.data argument widen exported data uri REDCap database API uri ... arguments passed `REDCapCAST::read_redcap_tables()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"data.frame list depending widen.data","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"Metadata can added editing data dictionary project initial design phase. want later add new instruments, function can used create () instrument(s) add project production.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"","code":"export_redcap_instrument(data, file, force = FALSE, record.id = \"record_id\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"data metadata relevant instrument. `ds2dd_detailed()` file destination file name. force force instrument creation ignore different form names just using first. record.id record id variable name. Default 'record_id'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"exports zip-file","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"","code":"# iris |> #  ds2dd_detailed( #    add.auto.id = TRUE, #    form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2)) #  ) |> #  purrr::pluck(\"meta\") |> #  (\\(.x){ #  split(.x, .x$form_name) #  })() |> #  purrr::imap(function(.x, .i){ #  export_redcap_instrument(.x,file=here::here(paste0(.i,Sys.Date(),\".zip\"))) #  })  # iris |> #  ds2dd_detailed( #    add.auto.id = TRUE #  ) |> #  purrr::pluck(\"meta\") |> #  export_redcap_instrument(file=here::here(paste0(\"instrument\",Sys.Date(),\".zip\")))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":null,"dir":"Reference","previous_headings":"","what":"Allows conversion of factor to numeric values preserving original levels — fct2num","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"Allows conversion factor numeric values preserving original levels","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"","code":"fct2num(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"numeric vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"","code":"c(1, 4, 3, \"A\", 7, 8, 1) |>   as_factor() |>   fct2num() #> Warning: invalid roman numeral: A #> [1] 1 2 3 4 5 6 1  structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |>   as_factor() |>   fct2num() #> [1]  1  2  3  2 10  9  structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"labelled\" ) |>   as_factor() |>   fct2num() #> [1]  1  2  3  2 10  9  # Outlier with labels, but no class of origin, handled like numeric vector # structure(c(1, 2, 3, 2, 10, 9), #   labels = c(Unknown = 9, Refused = 10) # ) |> #   as_factor() |> #   fct2num()  v <- sample(6:19, 20, TRUE) |> factor() dput(v) #> structure(c(7L, 1L, 10L, 3L, 10L, 10L, 9L, 8L, 3L, 2L, 6L, 8L,  #> 3L, 5L, 4L, 8L, 1L, 6L, 5L, 5L), levels = c(\"6\", \"7\", \"8\", \"9\",  #> \"11\", \"12\", \"13\", \"15\", \"16\", \"17\"), class = \"factor\") named_levels(v) #> 13  6 17  8 16 15  7 12 11  9  #>  7  1 10  3  9  8  2  6  5  4  fct2num(v) #>  [1] 13  6 17  8 17 17 16 15  8  7 12 15  8 11  9 15  6 12 11 11"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop unused levels preserving label data — fct_drop","title":"Drop unused levels preserving label data — fct_drop","text":"extends [forcats::fct_drop()] natively work across data.frame replace [base::droplevels()].","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop unused levels preserving label data — fct_drop","text":"","code":"fct_drop.data.frame(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop unused levels preserving label data — fct_drop","text":"x Factor drop unused levels ... arguments passed method.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRECATED Helper to import files correctly — file_extension","title":"DEPRECATED Helper to import files correctly — file_extension","text":"DEPRECATED Helper import files correctly","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRECATED Helper to import files correctly — file_extension","text":"","code":"file_extension(filenames)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRECATED Helper to import files correctly — file_extension","text":"filenames file names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRECATED Helper to import files correctly — file_extension","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DEPRECATED Helper to import files correctly — file_extension","text":"","code":"file_extension(list.files(here::here(\"\"))[[2]])[[1]] #> [1] \"\" file_extension(c(\"file.cd..ks\", \"file\")) #> [1] \"ks\" \"\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"focused_metadata — focused_metadata","title":"focused_metadata — focused_metadata","text":"Extracts limited metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"focused_metadata — focused_metadata","text":"","code":"focused_metadata(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"focused_metadata — focused_metadata","text":"metadata dataframe containing metadata vars_in_data Vector variable names dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"focused_metadata — focused_metadata","text":"dataframe containing metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":null,"dir":"Reference","previous_headings":"","what":"Sub-header formatting wrapper — format_subheader","title":"Sub-header formatting wrapper — format_subheader","text":"Sub-header formatting wrapper","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sub-header formatting wrapper — format_subheader","text":"","code":"format_subheader(data, tag = \"h2\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sub-header formatting wrapper — format_subheader","text":"data character vector tag character vector length 1","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sub-header formatting wrapper — format_subheader","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sub-header formatting wrapper — format_subheader","text":"","code":"\"Instrument header\" |> format_subheader() #> <div class=\"rich-text-field-label\"><h2>Instrument header<\/h2><\/div>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"Retrieve project API key stored, , set retrieve","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"","code":"get_api_key(key.name)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"key.name character vector key name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract attribute. Returns NA if none — get_attr","title":"Extract attribute. Returns NA if none — get_attr","text":"Extract attribute. Returns NA none","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract attribute. Returns NA if none — get_attr","text":"","code":"get_attr(data, attr = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract attribute. Returns NA if none — get_attr","text":"data vector attr attribute name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract attribute. Returns NA if none — get_attr","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract attribute. Returns NA if none — get_attr","text":"","code":"attr(mtcars$mpg, \"label\") <- \"testing\" do.call(c, sapply(mtcars, get_attr)) #> $mpg.label #> [1] \"testing\" #>  if (FALSE) { # \\dontrun{ mtcars |>   numchar2fct(numeric.threshold = 6) |>   ds2dd_detailed() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the id name — get_id_name","title":"Get the id name — get_id_name","text":"Get id name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the id name — get_id_name","text":"","code":"get_id_name(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the id name — get_id_name","text":"data data frame list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the id name — get_id_name","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess time variables based on naming pattern — guess_time_only","title":"Guess time variables based on naming pattern — guess_time_only","text":"repairing data time variables appended \"1970-01-01\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess time variables based on naming pattern — guess_time_only","text":"","code":"guess_time_only(   data,   validate.time = FALSE,   time.var.sel.pos = \"[Tt]i[d(me)]\",   time.var.sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess time variables based on naming pattern — guess_time_only","text":"data data.frame tibble validate.time Flag validate guessed time columns time.var.sel.pos Positive selection regex string passed `gues_time_only_filter()` sel.pos. time.var.sel.neg Negative selection regex string passed `gues_time_only_filter()` sel.neg.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess time variables based on naming pattern — guess_time_only","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Guess time variables based on naming pattern — guess_time_only","text":"","code":"redcapcast_data |> guess_time_only(validate.time = TRUE) #> $is.POSIX #> # A tibble: 25 × 2 #>    inclusion_time event_datetime      #>    <time>         <dttm>              #>  1 12:38:49       NA                  #>  2 10:38:57       NA                  #>  3       NA       NA                  #>  4       NA       2024-01-18 12:49:42 #>  5 12:01:07       NA                  #>  6       NA       NA                  #>  7       NA       NA                  #>  8       NA       2024-01-18 12:49:58 #>  9       NA       2024-01-18 12:50:01 #> 10       NA       2024-01-18 12:50:05 #> # ℹ 15 more rows #>  #> $is.datetime #> # A tibble: 25 × 1 #>    event_datetime      #>    <dttm>              #>  1 NA                  #>  2 NA                  #>  3 NA                  #>  4 2024-01-18 12:49:42 #>  5 NA                  #>  6 NA                  #>  7 NA                  #>  8 2024-01-18 12:49:58 #>  9 2024-01-18 12:50:01 #> 10 2024-01-18 12:50:05 #> # ℹ 15 more rows #>  #> $is.time_only #> # A tibble: 25 × 1 #>    inclusion_time #>    <time>         #>  1 12:38:49       #>  2 10:38:57       #>  3       NA       #>  4       NA       #>  5 12:01:07       #>  6       NA       #>  7       NA       #>  8       NA       #>  9       NA       #> 10       NA       #> # ℹ 15 more rows #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Try at determining which are true time only variables — guess_time_only_filter","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"just try guessing data type based data class column names hoping tiny bit naming consistency. R include time-data format natively, \"hms\" class `readr` used. converted character class REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"guess_time_only_filter(   data,   validate = FALSE,   sel.pos = \"[Tt]i[d(me)]\",   sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"data data set validate flag output validation data. output list. sel.pos Positive selection regex string sel.neg Negative selection regex string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"character vector list depending `validate` flag.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"data <- redcapcast_data data |> guess_time_only_filter() #> [1] \"inclusion_time\" data |>   guess_time_only_filter(validate = TRUE) |>   lapply(head) #> $is.POSIX #> # A tibble: 6 × 2 #>   inclusion_time event_datetime      #>   <time>         <dttm>              #> 1 12:38:49       NA                  #> 2 10:38:57       NA                  #> 3       NA       NA                  #> 4       NA       2024-01-18 12:49:42 #> 5 12:01:07       NA                  #> 6       NA       NA                  #>  #> $is.datetime #> # A tibble: 6 × 1 #>   event_datetime      #>   <dttm>              #> 1 NA                  #> 2 NA                  #> 3 NA                  #> 4 2024-01-18 12:49:42 #> 5 NA                  #> 6 NA                  #>  #> $is.time_only #> # A tibble: 6 × 1 #>   inclusion_time #>   <time>         #> 1 12:38:49       #> 2 10:38:57       #> 3       NA       #> 4       NA       #> 5 12:01:07       #> 6       NA       #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"Finish incomplete haven attributes substituting missings values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"","code":"haven_all_levels(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"data haven labelled variable","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"","code":"ds <- structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) haven::is.labelled(ds) #> [1] TRUE attributes(ds) #> $labels #> Unknown Refused  #>       9      10  #>  #> $class #> [1] \"haven_labelled\" #>  ds |> haven_all_levels() #>       1       2       3 Unknown Refused  #>       1       2       3       9      10"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":null,"dir":"Reference","previous_headings":"","what":"Change ","title":"Change ","text":"Change \"hms\" \"character\" REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change ","text":"","code":"hms2character(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change ","text":"data data set","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change ","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change ","text":"","code":"data <- redcapcast_data ## data |> time_only_correction() |> hms2character()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"Simple html tag wrapping REDCap text formatting","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"","code":"html_tag_wrap(data, tag = \"h2\", extra = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"data character vector tag character vector length 1 extra character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"","code":"html_tag_wrap(\"Titel\", tag = \"div\", extra = 'class=\"rich-text-field-label\"') #> <div class=\"rich-text-field-label\">Titel<\/div> html_tag_wrap(\"Titel\", tag = \"h2\") #> <h2>Titel<\/h2>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for multiple label classes — is.labelled","title":"Tests for multiple label classes — is.labelled","text":"Tests multiple label classes","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for multiple label classes — is.labelled","text":"","code":"is.labelled(   x,   classes = c(\"redcapcast_labelled\", \"haven_labelled\", \"labelled\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for multiple label classes — is.labelled","text":"x data classes classes test","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for multiple label classes — is.labelled","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tests for multiple label classes — is.labelled","text":"","code":"structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |> is.labelled() #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":null,"dir":"Reference","previous_headings":"","what":"Multi missing check — is_missing","title":"Multi missing check — is_missing","text":"Multi missing check","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multi missing check — is_missing","text":"","code":"is_missing(data, nas = c(\"\", \"NA\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multi missing check — is_missing","text":"data character vector nas character vector strings considered NA","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multi missing check — is_missing","text":"logical vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if repeatable or longitudinal — is_repeated_longitudinal","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"Test repeatable longitudinal","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(   data,   generics = c(\"redcap_event_name\", \"redcap_repeat_instrument\", \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"data data set generics default \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(c(\"record_id\", \"age\", \"record_id\", \"gender\")) #> [1] FALSE is_repeated_longitudinal(redcapcast_data) #> [1] TRUE is_repeated_longitudinal(list(redcapcast_data)) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":null,"dir":"Reference","previous_headings":"","what":"Completion marking based on completed upload — mark_complete","title":"Completion marking based on completed upload — mark_complete","text":"Completion marking based completed upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Completion marking based on completed upload — mark_complete","text":"","code":"mark_complete(upload, ls)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Completion marking based on completed upload — mark_complete","text":"upload output list `REDCapR::redcap_write()` ls output list `ds2dd_detailed()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Completion marking based on completed upload — mark_complete","text":"list `REDCapR::redcap_write()` results","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":null,"dir":"Reference","previous_headings":"","what":"Match fields to forms — match_fields_to_form","title":"Match fields to forms — match_fields_to_form","text":"Match fields forms","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match fields to forms — match_fields_to_form","text":"","code":"match_fields_to_form(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match fields to forms — match_fields_to_form","text":"metadata data frame containing field names form names vars_in_data character vector variable names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match fields to forms — match_fields_to_form","text":"data frame containing field names form names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"mtcars dataset slightly modified use Shiny app upload demonstration","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"","code":"data(mtcars_redcap)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"data frame 13 variables: record_id ID, numeric mpg ID, numeric cyl ID, numeric disp ID, numeric hp ID, numeric drat ID, numeric wt ID, numeric qsec ID, numeric vs ID, numeric ID, numeric gear ID, numeric carb ID, numeric name original rownames, charater","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get named vector of factor levels and values — named_levels","title":"Get named vector of factor levels and values — named_levels","text":"Get named vector factor levels values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get named vector of factor levels and values — named_levels","text":"","code":"named_levels(data, label = \"labels\", na.label = NULL, na.value = 99)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get named vector of factor levels and values — named_levels","text":"data factor label character string attribute named vector factor labels na.label character string refactor NA values. Default NULL. na.value new value NA strings. Ignored na.label NULL. Default 99.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get named vector of factor levels and values — named_levels","text":"named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get named vector of factor levels and values — named_levels","text":"","code":"if (FALSE) { # \\dontrun{ structure(c(1, 2, 3, 2, 10, 9),   labels = c(Unknown = 9, Refused = 10),   class = \"haven_labelled\" ) |>   as_factor() |>   named_levels() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":null,"dir":"Reference","previous_headings":"","what":"Nav_bar defining function for shiny ui — nav_bar_page","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"Nav_bar defining function shiny ui","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"","code":"nav_bar_page()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"shiny object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Applying var2fct across data set — numchar2fct","title":"Applying var2fct across data set — numchar2fct","text":"Individual thresholds character numeric columns","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applying var2fct across data set — numchar2fct","text":"","code":"numchar2fct(data, numeric.threshold = 6, character.throshold = 6)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applying var2fct across data set — numchar2fct","text":"data dataset. data.frame tibble numeric.threshold threshold var2fct numeric columns. Default 6. character.throshold threshold var2fct character columns. Default 6.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applying var2fct across data set — numchar2fct","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Applying var2fct across data set — numchar2fct","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ... if (FALSE) { # \\dontrun{ mtcars |>   numchar2fct(numeric.threshold = 6) |>   str() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper to auto-parse un-formatted data with haven and readr — parse_data","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"Helper auto-parse un-formatted data haven readr","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"","code":"parse_data(   data,   guess_type = TRUE,   col_types = NULL,   locale = readr::default_locale(),   ignore.vars = \"cpr\",   ... )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"data data.frame tibble guess_type logical guess type readr col_types specify col_types using readr semantics. Ignored guess_type TRUE locale option specify locale. Defaults readr::default_locale(). ignore.vars specify column names columns ignore parsing ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"","code":"mtcars |>   parse_data() |>   str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if vector can be interpreted as roman numerals — possibly_roman","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"Test vector can interpreted roman numerals","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"","code":"possibly_roman(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"data character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"","code":"sample(1:100, 10) |>   as.roman() |>   possibly_roman() #> [1] TRUE sample(c(TRUE, FALSE), 10, TRUE) |> possibly_roman() #> [1] FALSE rep(NA, 10) |> possibly_roman() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing character — process_user_input.character","title":"User input processing character — process_user_input.character","text":"User input processing character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing character — process_user_input.character","text":"","code":"# S3 method for class 'character' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing character — process_user_input.character","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing character — process_user_input.character","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing data.frame — process_user_input.data.frame","title":"User input processing data.frame — process_user_input.data.frame","text":"User input processing data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing data.frame — process_user_input.data.frame","text":"","code":"# S3 method for class 'data.frame' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing data.frame — process_user_input.data.frame","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing data.frame — process_user_input.data.frame","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing default — process_user_input.default","title":"User input processing default — process_user_input.default","text":"User input processing default","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing default — process_user_input.default","text":"","code":"# Default S3 method process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing default — process_user_input.default","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing default — process_user_input.default","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing — process_user_input","title":"User input processing — process_user_input","text":"User input processing","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing — process_user_input","text":"","code":"process_user_input(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing — process_user_input","text":"x input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing — process_user_input","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing response — process_user_input.response","title":"User input processing response — process_user_input.response","text":"User input processing response","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing response — process_user_input.response","text":"","code":"# S3 method for class 'response' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing response — process_user_input.response","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing response — process_user_input.response","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #>       id    ab   age   imm   vis   ver   att   del #>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1     1     1    74    38    35    30    29    35 #>  2     1     2    69    36    36    21    27    37 #>  3     2     1    63    32    31    26    34    38 #>  4     2     2    64    37    34    26    36    46 #>  5     3     1    69    39    33    31    47    29 #>  6     3     2    70    40    36    31    46    25 #>  7     4     1    79    44    37    20    37    36 #>  8     4     2    81    35    36    31    37    40 #>  9     5     1    77    35    26    17    20    36 #> 10     5     2    80    29    34    18    23    36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"Convenience function download complete instrument, using token storage keyring.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"","code":"read_redcap_instrument(   key,   uri,   instrument,   raw_or_label = \"raw\",   id_name = \"record_id\",   records = NULL )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"key key name standard keyring token retrieval. uri REDCap database API uri instrument instrument name raw_or_label raw label passed `REDCapR::redcap_read()` id_name id variable name. Default \"record_id\". records specify records download. Index numbers. Numeric vector.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Download REDCap data — read_redcap_tables","title":"Download REDCap data — read_redcap_tables","text":"Implementation REDCap_split focused data acquisition approach using REDCapR::redcap_read downloading specified fields, forms /events using built-focused_metadata including clean-. Works classical longitudinal projects without repeating instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download REDCap data — read_redcap_tables","text":"","code":"read_redcap_tables(   uri,   token,   records = NULL,   fields = NULL,   events = NULL,   forms = NULL,   raw_or_label = \"label\",   split_forms = \"all\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download REDCap data — read_redcap_tables","text":"uri REDCap database API uri token API token records records download fields fields download events events download forms forms download raw_or_label raw label tags. Can * \"raw\": Standard [REDCapR] method get raw values.   * \"label\": Standard [REDCapR] method get label values.   * \"\": Get raw values REDCap labels applied labels. Use   [as_factor()] format factors original labels use   [gtsummary] package easily get beautiful tables original labels   REDCap. Use [fct_drop()] drop empty levels. split_forms Whether split \"repeating\" \"\" forms, default .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download REDCap data — read_redcap_tables","text":"list instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download REDCap data — read_redcap_tables","text":"","code":"# Examples will be provided later"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":null,"dir":"Reference","previous_headings":"","what":"Redcap Wider — redcap_wider","title":"Redcap Wider — redcap_wider","text":"Converts list REDCap data frames long wide format. Handles longitudinal projects, yet repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Redcap Wider — redcap_wider","text":"","code":"redcap_wider(   data,   event.glue = \"{.value}_{redcap_event_name}\",   inst.glue = \"{.value}_{redcap_repeat_instance}\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Redcap Wider — redcap_wider","text":"data list data frames. event.glue dplyr::glue string repeated events naming inst.glue dplyr::glue string repeated instruments naming","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Redcap Wider — redcap_wider","text":"list data frames wide format.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Redcap Wider — redcap_wider","text":"","code":"# Longitudinal list1 <- list(   data.frame(     record_id = c(1, 2, 1, 2),     redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"),     age = c(25, 26, 27, 28)   ),   data.frame(     record_id = c(1, 2),     redcap_event_name = c(\"baseline\", \"baseline\"),     gender = c(\"male\", \"female\")   ) ) redcap_wider(list1) #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup gender #> 1         1           25           27   male #> 2         2           26           28 female # Simpel with two instruments list2 <- list(   data.frame(     record_id = c(1, 2),     age = c(25, 26)   ),   data.frame(     record_id = c(1, 2),     gender = c(\"male\", \"female\")   ) ) redcap_wider(list2) #> Joining with `by = join_by(record_id)` #>   record_id age gender #> 1         1  25   male #> 2         2  26 female # Simple with single instrument list3 <- list(data.frame(   record_id = c(1, 2),   age = c(25, 26) )) redcap_wider(list3) #>   record_id age #> 1         1  25 #> 2         2  26 # Longitudinal with repeatable instruments list4 <- list(   data.frame(     record_id = c(1, 2, 1, 2),     redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"),     age = c(25, 26, 27, 28)   ),   data.frame(     record_id = c(1, 1, 1, 1, 2, 2, 2, 2),     redcap_event_name = c(       \"baseline\", \"baseline\", \"followup\", \"followup\",       \"baseline\", \"baseline\", \"followup\", \"followup\"     ),     redcap_repeat_instrument = \"walk\",     redcap_repeat_instance = c(1, 2, 1, 2, 1, 2, 1, 2),     dist = c(40, 32, 25, 33, 28, 24, 23, 36)   ),   data.frame(     record_id = c(1, 2),     redcap_event_name = c(\"baseline\", \"baseline\"),     gender = c(\"male\", \"female\")   ) ) redcap_wider(list4) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup dist_1_baseline dist_1_followup #> 1         1           25           27              40              25 #> 2         2           26           28              28              23 #>   dist_2_baseline dist_2_followup gender #> 1              32              33   male #> 2              24              36 female"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data set for demonstration — redcapcast_data","title":"Data set for demonstration — redcapcast_data","text":"small dataset REDCap database demonstrational purposes. Contains synthetic data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data set for demonstration — redcapcast_data","text":"","code":"data(redcapcast_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data set for demonstration — redcapcast_data","text":"data frame 22 variables: record_id ID, numeric redcap_event_name Event name, character redcap_repeat_instrument Repeat instrument, character redcap_repeat_instance Repeat instance, numeric cpr CPR number, character inclusion Inclusion date, Date inclusion_time Inclusion time, hms dob Date birth, Date age Age decimal, numeric age_integer Age integer, numeric sex Legal sex, character cohabitation Cohabitation status, character con_calc con_calc con_mrs con_mrs consensus_complete consensus_complete hypertension Hypertension, character diabetes diabetes, character region region, character baseline_data_start_complete Completed, character mrs_assessed mRS Assessed, character mrs_date Assesment date, Date mrs_score Categorical score, numeric mrs_complete Complete, numeric event_datetime Event datetime, POSIXct event_age Age time event, numeric event_type Event type, character new_event_complete Completed, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCap metadata from data base — redcapcast_meta","title":"REDCap metadata from data base — redcapcast_meta","text":"metadata dataset REDCap database demonstration purposes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"REDCap metadata from data base — redcapcast_meta","text":"","code":"data(redcapcast_meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"REDCap metadata from data base — redcapcast_meta","text":"data frame 22 variables: field_name field_name, character form_name form_name, character section_header section_header, character field_type field_type, character field_label field_label, character select_choices_or_calculations select_choices_or_calculations, character field_note field_note, character text_validation_type_or_show_slider_number text_validation_type_or_show_slider_number, character text_validation_min text_validation_min, character text_validation_max text_validation_max, character identifier identifier, character branching_logic branching_logic, character required_field required_field, character custom_alignment custom_alignment, character question_number question_number, character matrix_group_name matrix_group_name, character matrix_ranking matrix_ranking, character field_annotation field_annotation, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace curly apostrophes and quotes from word — replace_curly_quote","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"Copied textclean, updated since 2018 CRAN. Github:https://github.com/trinker/textclean","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"","code":"replace_curly_quote(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"x character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Sanitize list of data frames — sanitize_split","title":"Sanitize list of data frames — sanitize_split","text":"Removing empty rows","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sanitize list of data frames — sanitize_split","text":"","code":"sanitize_split(   l,   generic.names = c(\"redcap_event_name\", \"redcap_repeat_instrument\",     \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sanitize list of data frames — sanitize_split","text":"l list data frames. generic.names vector generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sanitize list of data frames — sanitize_split","text":"list data frames generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Set attributes for named attribute. Appends if attr is NULL — set_attr","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"Set attributes named attribute. Appends attr NULL","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"","code":"set_attr(data, label, attr = NULL, overwrite = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"data vector label label attr attribute name overwrite overwrite existing attributes. Default FALSE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"vector attribute","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the included Shiny-app for database casting and upload — shiny_cast","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"Wraps shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"shiny_cast(...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"... Arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"# shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a data frame into separate tables for each form — split_non_repeating_forms","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"Split data frame separate tables form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"split_non_repeating_forms(table, universal_fields, fields)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"table data frame universal_fields character vector fields included every table fields two-column matrix containing names fields included form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"list data frames, one non-repeating form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"# Create a table table <- data.frame(   id = c(1, 2, 3, 4, 5),   form_a_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_a_age = c(25, 30, 25, 15, 20),   form_b_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_b_gender = c(\"M\", \"F\", \"M\", \"F\", \"F\") )  # Create the universal fields universal_fields <- c(\"id\")  # Create the fields fields <- matrix(   c(     \"form_a_name\", \"form_a\",     \"form_a_age\", \"form_a\",     \"form_b_name\", \"form_b\",     \"form_b_gender\", \"form_b\"   ),   ncol = 2, byrow = TRUE )  # Split the table split_non_repeating_forms(table, universal_fields, fields) #> $form_a_age #>   id #> 1  1 #> 2  2 #> 3  3 #> 4  4 #> 5  5 #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended string splitting — strsplitx","title":"Extended string splitting — strsplitx","text":"Can used substitute base function. Main claim fame easing split around defined delimiter, see example.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended string splitting — strsplitx","text":"","code":"strsplitx(x, split, type = \"classic\", perl = FALSE, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended string splitting — strsplitx","text":"x data split delimiter type Split type. Can c(\"classic\", \"\", \"\", \"around\") perl perl param strsplit() ... additional parameters passed base strsplit handling splits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended string splitting — strsplitx","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended string splitting — strsplitx","text":"","code":"test <- c(\"12 months follow-up\", \"3 steps\", \"mRS 6 weeks\", \"Counting to 231 now\") strsplitx(test, \"[0-9]\", type = \"around\") #> [[1]] #> [1] \"1\"                 \"2\"                 \" months follow-up\" #>  #> [[2]] #> [1] \"3\"      \" steps\" #>  #> [[3]] #> [1] \"mRS \"   \"6\"      \" weeks\" #>  #> [[4]] #> [1] \"Counting to \" \"2\"            \"3\"            \"1\"            \" now\"         #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":null,"dir":"Reference","previous_headings":"","what":"Correction based on time_only_filter function — time_only_correction","title":"Correction based on time_only_filter function — time_only_correction","text":"Correction based time_only_filter function","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correction based on time_only_filter function — time_only_correction","text":"","code":"time_only_correction(data, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correction based on time_only_filter function — time_only_correction","text":"data data set ... arguments passed `guess_time_only_filter()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correction based on time_only_filter function — time_only_correction","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correction based on time_only_filter function — time_only_correction","text":"","code":"data <- redcapcast_data ## data |> time_only_correction()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert vector to factor based on threshold of number of unique levels — var2fct","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"wrapper forcats::as_factor, sorts numeric vectors factoring, levels character vectors order appearance.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"","code":"var2fct(data, unique.n)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"data vector data.frame column unique.n threshold convert class factor","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"","code":"sample(seq_len(4), 20, TRUE) |>   var2fct(6) |>   summary() #> 1 2 3 4  #> 9 2 6 3  sample(letters, 20) |>   var2fct(6) |>   summary() #>    Length     Class      Mode  #>        20 character character  sample(letters[1:4], 20, TRUE) |> var2fct(6) #> Warning: invalid roman numerals: a b a a a a b #>  [1] c d c d a b d a d c a d a c c a b c d c #> Levels: c d a b"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"Named vector REDCap choices (`wrapping compact_vec()`)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"","code":"vec2choice(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"data named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"character string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"","code":"sample(seq_len(4), 20, TRUE) |>   as_factor() |>   named_levels() |>   sort() |>   vec2choice() #> [1] \"1, 1 | 2, 2 | 3, 3 | 4, 4\""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24114","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.4","title":"REDCapCAST 24.11.4","text":"release attempts solve problems hosting shiny_cast app, also implementing functions preserve much meta data possible REDCap database exporting data. hosting shinyapps.io given lot trouble recently. Modified package structure little around shiny_cast(), accommodate alternative hosting approach package functions included script instead requiring package. NEW: new option raw_or_label read_readcap_tables() added: “”. Get raw values REDCap labels applied labels. Use as_factor() format factors original labels use gtsummary package easily get beautiful tables original labels REDCap. Use fct_drop() drop empty levels. NEW: fct_drop() added extension forcats::fct_drop(), works across data.frames. Use fct_drop(). CHANGE: default data export method easy_redcap() changed use new labelled data export read_readcap_tables().","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24113","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.3","title":"REDCapCAST 24.11.3","text":"BUG: shiny_cast() fails load missed loading REDCapCAST library ui.r. Fixed. Tests great.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24112","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.2","title":"REDCapCAST 24.11.2","text":"CRAN release: 2024-11-22 24.11.1 rejected CRAN based wrong title capitalisation. opportunity extend package overhaul. actually turned major step towards usable shiny app received focus. implemented option specify categorical variables factorize, modified version {forcats} {haven}’s as_factor(), preserve attributes applied data able upload cast REDCap meta data richly formatted data (use .rds). matter input type, input parsed using default options {readr} package. Also avoid mis-labelling, logicals converted factors REDCap truefalse class follows different naming conversion compared R. Also correct support variable labels field labels (use .rds formatted data label labelled::var_label()) Vignettes documentation restructured. package detached REDCapRITS, originally forked . data split function kept, testing rewritten. projects evolved away original fork.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24111","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.1","title":"REDCapCAST 24.11.1","text":"Revised tests. Documentation slightly updated highlight shiny app casting REDCap metadata. working hosting Shiny Server.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-11-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 24.11.1","text":"Bug: ‘form.name’ specified ‘ds2dd_detailed()’ ignored. Corrected ignored ‘form.sep’ specified. Added handling re-occurring form.sep pattern. New: export_redcap_instrument() new version create_instrument_meta(), export single instrument. Multiple instrument export can done lapply() purrr::map(). allows inclusion functionality Shiny implementation easier handle. create_instrument_meta() deprecated. Improved: shiny_cast() app updated actually work install package clones whole repository.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"shiny-24-11-1","dir":"Changelog","previous_headings":"","what":"Shiny:","title":"REDCapCAST 24.11.1","text":"New: Major overhaul app interface introduction bslib building page. Also Detailed documentation added app workflow. New: Export REDCap instrument ready add database based uploaded spreadsheet. thanks export_redcap_instrument() function. functionality intended projects production adding instruments handled manually API upload. Bug: Export datadictionary “” instead “NA” NAs. Upload REDCap failed. anymore. shiny implementation included package. Implementing shinylive may looked later.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24103","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.10.3","title":"REDCapCAST 24.10.3","text":"CRAN release: 2024-10-03 Updated links spelling.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24101","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.10.1","title":"REDCapCAST 24.10.1","text":"Minor changes pass tests renv . rhub really running smooth previously.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2461","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.6.1","title":"REDCapCAST 24.6.1","text":"CRAN release: 2024-06-07","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-6-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.6.1","text":"Fix: read_redcap_tables(): field names testing allows include “[form_name]_complete” fields. Fix: ds2dd_detailed(): default record ID name now “record_id”, REDCap default. Default still use first column name. Support added interpret column name prefix suffix instrument names. See examples. New: create_instrument_meta(): creates zip instrument files allow adding new instruments project production. Takes data dictionary input creates zip instrument specified form_name column. New: doc2dd(): function convert document table data dictionary. allows specify instrument whole data dictionary text document, easier work easily modifiable. generic case data frame variable names values column. format like REDCap data dictionary, gives options formatting. related functions data handling formatting. One interesting function case_match_regex_list(), allows dynamic dplyr::case_when()-like approach regex-matching. think neat least.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-and-more-24-6-1","dir":"Changelog","previous_headings":"","what":"Documentation and more","title":"REDCapCAST 24.6.1","text":"Dependencies: order deploy shiny_cast() shinylive, need remove curl dependency. accomplish , shiny_deploy() helper functions moved package project.aid. realising REDCapR curl dependency, culprit. REDCapCAST going shinylive web-app without removing REDCapR dependency REDCap database interaction, defy purpose. ’ll stick hosted Shiny app instead.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2421","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.2.1","title":"REDCapCAST 24.2.1","text":"CRAN release: 2024-02-28","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-2-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.2.1","text":"Fix: ds2dd(): uses correct default dd column names. deprecated. Fix: easy_redcap(): fixed actually allow project naming. also specifically asks uri. widening updated work. Fix: redcap_wider(): updated accept formats allow handling simple projects without repeating instruments longitudinal. Fix: read_redcap_tables(): now handles non-longitudinal project without repeatable instruments. NEW: ds2dd_detailed(): extension ds2dd(), serves preserve much metadata possible automatically. Depends group helper functions also introduced. special note guess_time_only_filter(), try guess columns/variables formatted time formats. Supports hms time format. DETAILED INSTRUCTION VIGNETTE PENDING. NEW: read_redcap_instrument(): convenience function retrieve complete instrument. Goes little focused approach. REDCapR::redcap_read() can specify form download. also specify record id variable though. done read_redcap_instrument(). Nothing fancy. NEW: shiny_cast(): Shiny application ease process converting spreadsheet/data set REDCap database. app runs locally data transferred securely. can just create upload data dictionary, can also transfer given data process. plan host app shinyapps.io, now can run locally.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"other-24-2-1","dir":"Changelog","previous_headings":"","what":"Other","title":"REDCapCAST 24.2.1","text":"believe renv now added runs correctly. clone, renv::restore() install necessary package modify package. seems always back forth. renv may way . Added Code Conduct.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2411","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.1.1","title":"REDCapCAST 24.1.1","text":"CRAN release: 2024-01-09","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-1-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.1.1","text":"Fix: read_redcap_tables(): checking form names based data dictionary allow handling non-longitudinal projects. Prints invalid form names invalid event names. invalid form names supplied REDCapR::redcap_read() (backbone), forms exported, want focused approach. Invalid event names give output rather peculiar formatting. Checking field names validity also added.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-23121","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.12.1","title":"REDCapCAST 23.12.1","text":"CRAN release: 2023-12-20 One new function ease secure dataset retrieval bug fixes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-12-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.12.1","text":"New: easy_redcap() function ease retrieval dataset read_redcap_tables() keyring-package based key storage, handles secure API set, storage retrieval. Relies small helper function, get_api_key(), wraps relevant keyring-functions. Includes option cast data wide format flag widen.data. Fix: REDCap_split(): using function , supplying data set check boxes fail metadata supplied tibble. Metadata now converted data.frame. Fixed. Fix: read_redcap_tables(): fixed bug supplying events.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2362","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.2","title":"REDCapCAST 23.6.2","text":"CRAN release: 2023-07-04 version marks introduction helper functions handle database creation.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-6-2","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.6.2","text":"New: ds2dd() function migrating stRoke-package. Assists building data dictionary REDCap dataset. New: strsplitx() function ease string splitting extension base::strsplit(). Inspiration https://stackoverflow.com//11014253/21019325 https://www.r-bloggers.com/2018/04/strsplit--keeping--delimiter/. New: d2n() function converts single digits written numbers. Used sanitize variable form names REDCap database creation. universal number word suggest english::word() xfun::numbers_to_words(), though testing .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2361","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.1","title":"REDCapCAST 23.6.1","text":"CRAN release: 2023-06-06","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-6-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.6.1","text":"Updated description. Look! hex icon! Heading CRAN.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-4-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.4.1","text":"Aiming CRAN","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-3-2","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.3.2","text":"Page added. Vignettes follow. GithubActions tests added code coverage assessed. Badge galore..","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"new-name-redcapcast-23-3-1","dir":"Changelog","previous_headings":"","what":"New name: REDCapCAST","title":"REDCapCAST 23.3.1","text":"reflect new functions limitation working R, changed naming fork, still, course, maintaining status fork. versioning moved monthly naming convention. main goal package keep option export defined subset whole dataset REDCap server made possible REDCapR::redcap_read() function, combine work put REDCapRITS package handling longitudinal projects /projects repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-3-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 23.3.1","text":"read_redcap_tables() NEW: function mainly implementation combined use REDCapR::readcap_read() REDCap_split() maintain focused nature REDCapR::readcap_read(), download specified data. Also implements tests valid form names event names. usual fall-back solution get data. redcap_wider() NEW: function pivots long data frames read_redcap_tables() using tidyr::pivot_wider(). focused_metadata() NEW: hidden helper function enable focused data acquisition approach handle subset metadata corresponding focused dataset.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"notes-23-3-1","dir":"Changelog","previous_headings":"","what":"Notes:","title":"REDCapCAST 23.3.1","text":"metadata handling IMPROVED: improved handling different column names matadata (DataDictionary) REDCap dependent whether acquired thorugh api og downloaded server.","code":""}]