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< img src = "" class = "logo" alt = "" > < h1 > ds2dd< / h1 >
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< h4 data-toc-skip class = "date" > 2023-04-13< / h4 >
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< small class = "dont-index" > Source: < a href = "https://github.com/agdamsbo/stRoke/blob/HEAD/vignettes/ds2dd.Rmd" class = "external-link" > < code > vignettes/ds2dd.Rmd< / code > < / a > < / small >
< div class = "d-none name" > < code > ds2dd.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://agdamsbo.github.io/stRoke/" class = "external-link" > stRoke< / a > < / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< div class = "section level2" >
< h2 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 >
< / h2 >
< p > This function can be used as a simple tool for creating at data base
metadata file for REDCap (called a DataDictionary) based on a given data
set file.< / p >
< div class = "section level3" >
< h3 id = "step-1---load-your-data-set" > Step 1 - Load your data set< a class = "anchor" aria-label = "anchor" href = "#step-1---load-your-data-set" > < / a >
< / h3 >
< p > Here we’
package.< / p >
< div class = "sourceCode" id = "cb2" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/data.html" class = "external-link" > data< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "talos"< / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "va" > ds< / span > < span class = "op" > < -< / span > < span class = "va" > talos< / span > < / span >
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< span > < span class = "co" > # As the data set lacks an ID column, one is added< / span > < / span >
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< span > < span class = "va" > ds< / span > < span class = "op" > $< / span > < span class = "va" > id< / span > < 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" > < a href = "https://rdrr.io/r/base/nrow.html" class = "external-link" > nrow< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ds< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< / div >
< div class = "section level3" >
< h3 id = "step-2---create-the-datadictionary" > Step 2 - Create the DataDictionary< a class = "anchor" aria-label = "anchor" href = "#step-2---create-the-datadictionary" > < / a >
< / h3 >
< div class = "sourceCode" id = "cb3" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "va" > datadictionary< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/ds2dd.html" > ds2dd< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ds< / span > ,record.id < span class = "op" > =< / span > < span class = "st" > "id"< / span > ,include.column.names < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< p > Now additional specifications to the DataDictionary can be made
manually, or it can be uploaded and modified manually in the graphical
user interface on the web page.< / p >
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< p > The function will transform column names to lower case and substitute
spaces for underscores. The output is a list with the DataDictionary and
a vector of new column names for the dataset to fit the meta data.< / p >
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< / div >
< div class = "section level3" >
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< h3 id = "step-3---meta-data-upload" > Step 3 - Meta data upload< a class = "anchor" aria-label = "anchor" href = "#step-3---meta-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" >
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< 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" > datadictionary< / span > < span class = "op" > $< / span > < span class = "va" > DataDictionary< / span > ,< span class = "st" > "datadictionary.csv"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< / 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 >
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< span > < span class = "va" > datadictionary< / span > < span class = "op" > $< / span > < span class = "va" > DataDictionary< / span > ,< / span >
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< span > redcap_uri < span class = "op" > =< / span > < span class = "fu" > keyring< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/keyring/man/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://rdrr.io/pkg/keyring/man/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
< code > < a href = "https://r-lib.github.io/keyring/index.html" class = "external-link" > library(keyring)< / a > < / code > to store credentials in < a href = "https://agdamsbo.github.io/redcap-r-handbook/access.html#sec-getting-access" class = "external-link" > chapter
1.1< / a > .< / p >
< / div >
< / div >
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< 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 og 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 = "co" > # new column nams are applied< / span > < / span >
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ds< / span > < span class = "op" > )< / span > < span class = "op" > < -< / span > < span class = "va" > datadictionary< / span > < span class = "op" > $< / span > < span class = "va" > `Column names`< / span > < / span >
< span > < / span >
< 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" > ds< / span > ,< / span >
< span > redcap_uri < span class = "op" > =< / span > < span class = "fu" > keyring< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/keyring/man/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://rdrr.io/pkg/keyring/man/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 >
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< p > Developed by Andreas Gammelgaard Damsbo.< / p >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 2.0.7.< / p >
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