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< img src = "../logo.png" class = "logo" alt = "" > < h1 > Database-creation< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/agdamsbo/REDCapCAST/blob/main/vignettes/Database-creation.Rmd" class = "external-link" > < code > vignettes/Database-creation.Rmd< / code > < / a > < / small >
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< div class = "d-none name" > < code > Database-creation.Rmd< / code > < / div >
< / div >
< div class = "sourceCode" id = "cb1" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://github.com/agdamsbo/REDCapCAST" class = "external-link" > REDCapCAST< / a > < / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< div class = "section level2" >
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< h2 id = "two-different-ways-to-create-a-data-base" > Two different ways to create a data base< a class = "anchor" aria-label = "anchor" href = "#two-different-ways-to-create-a-data-base" > < / a >
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< / h2 >
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< p > < code > REDCapCAST< / code > provides two approaches to creating a data
dictionary aimed at helping out in two different cases:< / p >
< ol style = "list-style-type: decimal" >
< li > < p > Easily create a REDCap data base from an existing data
set.< / p > < / li >
< li > < p > Create a table in Word describing a variables in a data base and
use this to create a data base.< / p > < / li >
< / ol >
< p > In the following I will try to come with a few suggestions on how to
use these approaches.< / p >
< div class = "section level3" >
< h3 id = "easy-data-set-to-data-base-workflow" > Easy data set to data base workflow< a class = "anchor" aria-label = "anchor" href = "#easy-data-set-to-data-base-workflow" > < / a >
< / h3 >
< p > The first iteration of a dataset to data dictionary function is the
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< code > < a href = "../reference/ds2dd.html" > ds2dd()< / a > < / code > , which creates a very basic data dictionary with
all variables stored as text. This is sufficient for just storing old
datasets/spreadsheets securely in REDCap.< / p >
< div class = "sourceCode" id = "cb2" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "va" > d1< / span > < span class = "op" > < -< / span > < span class = "va" > mtcars< / span > < span class = "op" > |> < / span > < / span >
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< span > < span class = "fu" > dplyr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > record_id < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/seq.html" class = "external-link" > seq_len< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > dplyr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/context.html" class = "external-link" > n< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > |> < / span > < / span >
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< span > < span class = "fu" > < a href = "../reference/ds2dd.html" > ds2dd< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "va" > d1< / span > < span class = "op" > |> < / span > < / span >
< span > < span class = "fu" > gt< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://gt.rstudio.com/reference/gt.html" class = "external-link" > gt< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< p > The more advanced < code > < a href = "../reference/ds2dd_detailed.html" > ds2dd_detailed()< / a > < / code > is a natural
development. It will try to apply the most common data classes for data
validation and will assume that the first column is the id number. It
outputs a list with the dataset with modified variable names to comply
with REDCap naming conventions and a data dictionary.< / p >
< p > The dataset should be correctly formatted for the data dictionary to
preserve as much information as possible.< / p >
< div class = "sourceCode" id = "cb3" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "va" > d2< / span > < span class = "op" > < -< / span > < span class = "fu" > REDCapCAST< / span > < span class = "fu" > ::< / span > < span class = "va" > < a href = "../reference/redcapcast_data.html" > redcapcast_data< / a > < / span > < span class = "op" > |> < / span > < / span >
< span > < span class = "fu" > dplyr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > record_id < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/seq.html" class = "external-link" > seq_len< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > dplyr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/context.html" class = "external-link" > n< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span >
< span > region< span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/factor.html" class = "external-link" > factor< / a > < / span > < span class = "op" > (< / span > < span class = "va" > region< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > |> < / span > < / span >
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< span > < span class = "fu" > dplyr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > record_id< / span > , < span class = "fu" > dplyr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/everything.html" class = "external-link" > everything< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > |> < / span > < / span >
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< span > < span class = "op" > (< / span > \< span class = "op" > (< / span > < span class = "va" > .x< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span >
< span > < span class = "va" > .x< / span > < span class = "op" > [< / span > < span class = "op" > !< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/grep.html" class = "external-link" > grepl< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "_complete$"< / span > ,< span class = "fu" > < a href = "https://rdrr.io/r/base/names.html" class = "external-link" > names< / a > < / span > < span class = "op" > (< / span > < span class = "va" > .x< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span > < / span >
< span > < span class = "op" > }< / span > < span class = "op" > )< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > |> < / span > < / span >
< span > < span class = "op" > (< / span > \< span class = "op" > (< / span > < span class = "va" > .x< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span >
< span > < span class = "va" > .x< / span > < span class = "op" > [< / span > < span class = "op" > !< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/grep.html" class = "external-link" > grepl< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "^redcap"< / span > ,< span class = "fu" > < a href = "https://rdrr.io/r/base/names.html" class = "external-link" > names< / a > < / span > < span class = "op" > (< / span > < span class = "va" > .x< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span > < / span >
< span > < span class = "op" > }< / span > < span class = "op" > )< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > |> < / span > < / span >
< span > < span class = "fu" > < a href = "../reference/ds2dd_detailed.html" > ds2dd_detailed< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > |> < / span > < / span >
< span > < span class = "fu" > purrr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://purrr.tidyverse.org/reference/pluck.html" class = "external-link" > pluck< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "meta"< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "va" > d2< / span > < span class = "op" > |> < / span > < / span >
< span > < span class = "fu" > gt< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://gt.rstudio.com/reference/gt.html" class = "external-link" > gt< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< p > Additional specifications to the DataDictionary can be made manually,
or it can be uploaded and modified manually in the graphical user
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interface on the REDCap server.< / p >
< / div >
< div class = "section level3" >
< h3 id = "data-base-from-table" > Data base from table< a class = "anchor" aria-label = "anchor" href = "#data-base-from-table" > < / a >
< / h3 >
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< p > …instructions and examples are coming…< / p >
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< / div >
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< div class = "section level3" >
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< h3 id = "meta-data-and-data-upload" > Meta data and data upload< a class = "anchor" aria-label = "anchor" href = "#meta-data-and-data-upload" > < / a >
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< / h3 >
< p > Now the DataDictionary can be exported as a spreadsheet and uploaded
or it can be uploaded using the < code > REDCapR< / code > package (only
projects with “Development” status).< / p >
< p > Use one of the two approaches below:< / p >
< div class = "section level4" >
< h4 id = "manual-upload" > Manual upload< a class = "anchor" aria-label = "anchor" href = "#manual-upload" > < / a >
< / h4 >
< div class = "sourceCode" id = "cb4" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/write.table.html" class = "external-link" > write.csv< / a > < / span > < span class = "op" > (< / span > < span class = "va" > dd_ls< / span > < span class = "op" > $< / span > < span class = "va" > meta< / span > , < span class = "st" > "datadictionary.csv"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level4" >
< h4 id = "upload-with-redcapr" > Upload with < code > REDCapR< / code > < a class = "anchor" aria-label = "anchor" href = "#upload-with-redcapr" > < / a >
< / h4 >
< div class = "sourceCode" id = "cb5" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > REDCapR< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://ouhscbbmc.github.io/REDCapR/reference/redcap_metadata_write.html" class = "external-link" > redcap_metadata_write< / a > < / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > dd_ls< / span > < span class = "op" > $< / span > < span class = "va" > meta< / span > ,< / span >
< span > redcap_uri < span class = "op" > =< / span > < span class = "fu" > keyring< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://keyring.r-lib.org/reference/key_get.html" class = "external-link" > key_get< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "DB_URI"< / span > < span class = "op" > )< / span > ,< / span >
< span > token < span class = "op" > =< / span > < span class = "fu" > keyring< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://keyring.r-lib.org/reference/key_get.html" class = "external-link" > key_get< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "DB_TOKEN"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > In the < a href = "https://agdamsbo.github.io/redcap-r-handbook/" class = "external-link" > “REDCap R
Handbook”< / a > more is written on interfacing with REDCap in R using the
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< code > < a href = "https://keyring.r-lib.org/" class = "external-link" > library(keyring)< / a > < / code > to store credentials in < a href = "https://agdamsbo.github.io/redcap-r-handbook/doc/access.html#sec-getting-access" class = "external-link" > chapter
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1.1< / a > .< / p >
< / div >
< / div >
< div class = "section level3" >
< h3 id = "step-4---data-upload" > Step 4 - Data upload< a class = "anchor" aria-label = "anchor" href = "#step-4---data-upload" > < / a >
< / h3 >
< p > The same two options are available for data upload as meta data
upload: manual or through < code > REDCapR< / code > .< / p >
< p > Only the latter is shown here.< / p >
< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > REDCapR< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://ouhscbbmc.github.io/REDCapR/reference/redcap_write.html" class = "external-link" > redcap_write< / a > < / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > dd_ls< / span > < span class = "op" > $< / span > < span class = "va" > data< / span > ,< / span >
< span > redcap_uri < span class = "op" > =< / span > < span class = "fu" > keyring< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://keyring.r-lib.org/reference/key_get.html" class = "external-link" > key_get< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "DB_URI"< / span > < span class = "op" > )< / span > ,< / span >
< span > token < span class = "op" > =< / span > < span class = "fu" > keyring< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://keyring.r-lib.org/reference/key_get.html" class = "external-link" > key_get< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "DB_TOKEN"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< / div >
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< / main > < aside class = "col-md-3" > < nav id = "toc" aria-label = "Table of contents" > < h2 > On this page< / h2 >
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< / nav > < / aside >
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< footer > < div class = "pkgdown-footer-left" >
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< p > Developed by Andreas Gammelgaard Damsbo, Paul Egeler.< / p >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 2.1.1.< / p >
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< / div >
< / footer >
< / div >
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< / body >
< / html >
