From ffec8f645aea966e0818d0048b5ab8221e128f3b Mon Sep 17 00:00:00 2001 From: agdamsbo <43278243+agdamsbo@users.noreply.github.com> Date: Tue, 19 Nov 2024 12:20:19 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20agdamsbo?= =?UTF-8?q?/REDCapCAST@42efec437a71ab730cf0495c9cad3e85ac0bd736=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- index.html | 4 ++-- news/index.html | 2 +- pkgdown.yml | 2 +- reference/REDCapCAST-package.html | 9 ++++----- reference/haven_all_levels.html | 4 ++-- search.json | 2 +- 6 files changed, 11 insertions(+), 12 deletions(-) diff --git a/index.html b/index.html index e44b3d2..369c8b5 100644 --- a/index.html +++ b/index.html @@ -17,8 +17,8 @@ - - + + diff --git a/news/index.html b/news/index.html index 21b894f..de236ea 100644 --- a/news/index.html +++ b/news/index.html @@ -40,7 +40,7 @@

REDCapCAST 24.11.2

24.11.1 was rejected on CRAN based on wrong title capitalisation. This was an opportunity to extend the package overhaul.

-

Documentation has been updated. Data parser functions have been added (based on readr) and separated from the ds2dd_detailed().

+

Documentation has been updated. Data parser functions have been added (based on readr) and separated from the ds2dd_detailed(). Now also includes conversion of logicals to factor as REDCap truefalse class follows different naming conversion compared to R. Also correct support for variable labels as field labels (use .rds formatted data and label with labelled::var_label())

Vignettes and documentation have been restructured.

This package has been detached from the REDCapRITS, which it was originally forked from. The data split function will be kept, while testing will be rewritten. This projects has evolved away from the original fork, so I think this detachment is fair.

diff --git a/pkgdown.yml b/pkgdown.yml index b73488d..bc120aa 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: 2024-11-19T12:05Z +last_built: 2024-11-19T12:19Z urls: reference: https://agdamsbo.github.io/REDCapCAST/reference article: https://agdamsbo.github.io/REDCapCAST/articles diff --git a/reference/REDCapCAST-package.html b/reference/REDCapCAST-package.html index b4ac5f9..22bcf11 100644 --- a/reference/REDCapCAST-package.html +++ b/reference/REDCapCAST-package.html @@ -1,9 +1,9 @@ REDCapCAST: REDCap Castellated Data Handling and Metadata Casting — REDCapCAST-package • REDCapCAST Skip to contents @@ -46,7 +46,7 @@ Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See https://gi

-

Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See https://github.com/pegeler/REDCapRITS. 'REDCap' database casting and handling of castellated data when using repeated instruments and longitudinal projects. Keeps a focused data export approach, by allowing to only export required data from the database. Also for casting new REDCap databases based on datasets from other sources. 'REDCap' (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with external sources (Harris et al (2009) doi:10.1016/j.jbi.2008.08.010 +

Casting metadata for REDCap database creation and handling of castellated data using repeated instruments and longitudinal projects in 'REDCap'. Keeps a focused data export approach, by allowing to only export required data from the database. Also for casting new REDCap databases based on datasets from other sources. Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See https://github.com/pegeler/REDCapRITS. 'REDCap' (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with 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 ).

@@ -62,8 +62,7 @@ Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See https://gi

Author

Maintainer: Andreas Gammelgaard Damsbo agdamsbo@clin.au.dk (ORCID)

-

Authors:

+ diff --git a/reference/haven_all_levels.html b/reference/haven_all_levels.html index a9d5b05..3f477fa 100644 --- a/reference/haven_all_levels.html +++ b/reference/haven_all_levels.html @@ -66,8 +66,8 @@ labels = c(Unknown = 9, Refused = 10), class = "haven_labelled" ) -labelled::is.labelled(ds) -#> Error in loadNamespace(x): there is no package called ‘labelled’ +haven::is.labelled(ds) +#> [1] TRUE attributes(ds) #> $labels #> Unknown Refused diff --git a/search.json b/search.json index e632768..2fc76d4 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"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. 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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 . 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 .","code":" Copyright (C) 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 . Copyright (C) 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\")= #> $ 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\")= #> $ 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\")= #> $ 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\")="},{"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 Castellated Data Handling Metadata Casting. R package version 24.11.2, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{, title = {REDCapCAST: REDCap Castellated Data Handling and Metadata Casting}, author = {Andreas Gammelgaard Damsbo and Paul Egeler}, year = {2024}, note = {R package version 24.11.2, 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 Castellated Data Handling and Metadata Casting","title":"REDCap Castellated Data Handling and Metadata Casting","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 Castellated Data Handling and Metadata Casting","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 Castellated Data Handling and Metadata Casting","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 Castellated Data Handling and Metadata Casting","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 Castellated Data Handling and Metadata Casting","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 Castellated Data Handling and Metadata Casting — REDCapCAST-package","title":"REDCapCAST: REDCap Castellated Data Handling and Metadata Casting — REDCapCAST-package","text":"Originally forked R part 'REDCapRITS' Paul Egeler. See https://github.com/pegeler/REDCapRITS. 'REDCap' database casting handling castellated data using repeated instruments longitudinal projects. Keeps focused data export approach, allowing export required data database. Also casting new REDCap databases based datasets sources. '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 Castellated Data Handling and Metadata Casting — 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/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/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_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/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]\")) #>
Patient ID
<\/span><\/h5> <\/td>
[cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> create_html_table(text = paste(\"assessor\", 1:2, sep = \"_\"), variable = c(\"[cpr]\")) #>
assessor_1
<\/span><\/h5> <\/td>
[cpr]<\/span><\/h5> <\/td> <\/tr>
assessor_2
<\/span><\/h5> <\/td>
[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":"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\") #> A default id column has been added # 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 #> # A tibble: 150 × 5 #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> 7 4.6 3.4 1.4 0.3 setosa #> 8 5 3.4 1.5 0.2 setosa #> 9 4.4 2.9 1.4 0.2 setosa #> 10 4.9 3.1 1.5 0.1 setosa #> # ℹ 140 more rows #> #> $meta #> # A tibble: 5 × 18 #> field_name form_name section_header field_type field_label #> #> 1 Sepal.Length b NA text Sepal.Length #> 2 Sepal.Width b NA text Sepal.Width #> 3 Petal.Length b NA text Petal.Length #> 4 Petal.Width b NA text Petal.Width #> 5 Species b NA radio Species #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> # 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 = metadata_names )"},{"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 REDCapCAST::metadata_names.","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 REDCapCAST:::metadata_names. 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":"data <- REDCapCAST::redcapcast_data data |> ds2dd_detailed() #> $data #> # A tibble: 25 × 27 #> record_id redcap_event_name redcap_repeat_instrument redcap_repeat_instance #> #> 1 1 inclusion NA NA #> 2 2 inclusion NA NA #> 3 2 follow1 NA NA #> 4 2 follow1 New Event (?) 1 #> 5 3 inclusion NA NA #> 6 3 follow1 NA NA #> 7 3 follow2 NA NA #> 8 3 follow1 New Event (?) 1 #> 9 3 follow1 New Event (?) 2 #> 10 3 follow2 New Event (?) 1 #> # ℹ 15 more rows #> # ℹ 23 more variables: cpr , inclusion , inclusion_time , #> # dob , age , age_integer , sex , cohabitation , #> # hypertension , diabetes , region , #> # baseline_data_start_complete , mrs_assessed , mrs_date , #> # mrs_score , mrs_complete , con_mrs , con_calc , #> # consensus_complete , event_datetime , event_age , … #> #> $meta #> # A tibble: 27 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id data NA text record_id #> 2 redcap_event_name data NA text redcap_event_na… #> 3 redcap_repeat_instrument data NA text redcap_repeat_i… #> 4 redcap_repeat_instance data NA text redcap_repeat_i… #> 5 cpr data NA text cpr #> 6 inclusion data NA text inclusion #> 7 inclusion_time data NA text inclusion_time #> 8 dob data NA text dob #> 9 age data NA text age #> 10 age_integer data NA text age_integer #> # ℹ 17 more rows #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> iris |> ds2dd_detailed(add.auto.id = TRUE) #> A default id column has been added #> $data #> # A tibble: 150 × 6 #> record_id sepal.length sepal.width petal.length petal.width species #> #> 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 #> #> 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 , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> 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 default id column has been added #> # A tibble: 6 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id c NA text record_id #> 2 sepal.length b NA text sepal.length #> 3 sepal.width b NA text sepal.width #> 4 petal.length b NA text petal.length #> 5 petal.width c NA text petal.width #> 6 species c NA radio species #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation mtcars |> ds2dd_detailed(add.auto.id = TRUE) #> A default id column has been added #> $data #> # A tibble: 32 × 12 #> record_id mpg cyl disp hp drat wt qsec vs am gear carb #> #> 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 #> #> 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 , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> data <- iris |> ds2dd_detailed(add.auto.id = TRUE) |> purrr::pluck(\"data\") #> A default id column has been added 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 #> #> 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 #> #> 1 record_id b NA text record_id #> 2 sepal.length b NA text sepal.length #> 3 sepal.width b NA text sepal.width #> 4 petal.length b NA text petal.length #> 5 petal.width b NA text petal.width #> 6 species b NA radio species #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #>"},{"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/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() #>

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\" sapply(mtcars, get_attr) #> $mpg #> $mpg$label #> [1] \"testing\" #> #> #> $cyl #> NULL #> #> $disp #> NULL #> #> $hp #> NULL #> #> $drat #> NULL #> #> $wt #> NULL #> #> $qsec #> NULL #> #> $vs #> NULL #> #> $am #> NULL #> #> $gear #> NULL #> #> $carb #> NULL #> lapply(mtcars, \\(.x)get_attr(.x, NULL)) #> $mpg #> $mpg$label #> [1] \"testing\" #> #> #> $cyl #> NULL #> #> $disp #> NULL #> #> $hp #> NULL #> #> $drat #> NULL #> #> $wt #> NULL #> #> $qsec #> NULL #> #> $vs #> NULL #> #> $am #> NULL #> #> $gear #> NULL #> #> $carb #> NULL #> mtcars |> numchar2fct(numeric.threshold = 6) |> ds2dd_detailed() #> $data #> # A tibble: 32 × 11 #> mpg cyl disp hp drat wt qsec vs am gear carb #> #> 1 21 6 160 110 3.9 2.62 16.5 0 1 4 4 #> 2 21 6 160 110 3.9 2.88 17.0 0 1 4 4 #> 3 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1 #> 4 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1 #> 5 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2 #> 6 18.1 6 225 105 2.76 3.46 20.2 1 0 3 1 #> 7 14.3 8 360 245 3.21 3.57 15.8 0 0 3 4 #> 8 24.4 4 147. 62 3.69 3.19 20 1 0 4 2 #> 9 22.8 4 141. 95 3.92 3.15 22.9 1 0 4 2 #> 10 19.2 6 168. 123 3.92 3.44 18.3 1 0 4 4 #> # ℹ 22 more rows #> #> $meta #> # A tibble: 11 × 18 #> field_name form_name section_header field_type field_label #> #> 1 mpg data NA text testing #> 2 cyl data NA radio cyl #> 3 disp data NA text disp #> 4 hp data NA text hp #> 5 drat data NA text drat #> 6 wt data NA text wt #> 7 qsec data NA text qsec #> 8 vs data NA radio vs #> 9 am data NA radio am #> 10 gear data NA radio gear #> 11 carb data NA radio carb #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #>"},{"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 #>