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ezraporterezraporter
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prep for 1.2.3
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‎DESCRIPTION

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Package: REDCapTidieR
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Type: Package
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Title: Extract 'REDCap' Databases into Tidy 'Tibble's
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Version: 1.2.2.9000
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Version: 1.2.3
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Authors@R: c(
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person("Richard", "Hanna", , "hannar1@chop.edu", role = c("aut", "cre"),
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comment = c(ORCID = "0009-0005-6496-8154")),

‎NEWS.md

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# REDCapTidieR (development version)
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# REDCapTidieR 1.2.3
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- Fixed a bug causing `read_redcap()` to incorrectly report categorical variables with data values that don't match any options in the metadata.
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- Fixed a bug causing `read_redcap()` to fail with an unhelpful error when attempting to export DAG information for a user with insufficient DAG export privileges.
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# REDCapTidieR 1.2.2
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‎R/write.R

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@@ -230,7 +230,7 @@ add_labelled_xlsx_features <- function(supertbl,
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supertbl_toc = NULL) {
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check_installed("labelled", reason = "to make use of labelled features in `write_redcap_xlsx`")
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# Generate variable labels off of labelled dictionary objects ----
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generate_dictionaries <- function(x) { #nolint: object_usage_linter
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generate_dictionaries <- function(x) { # nolint: object_usage_linter
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labelled::generate_dictionary(x) %>%
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select("variable", "label") %>%
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mutate(label = if_else(is.na(.data$label), "", .data$label)) %>%
@@ -284,7 +284,7 @@ add_labelled_xlsx_features <- function(supertbl,
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}
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# Define redcap_data variable labels
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var_labels <- map(.x = supertbl$redcap_data, ~generate_dictionaries(.x))
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var_labels <- map(.x = supertbl$redcap_data, ~ generate_dictionaries(.x))
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for (i in seq_along(supertbl$redcap_form_name)) {
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wb$add_data(

‎cran-comments.md

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Thank you for taking the time to review this submission and please reach out to either Stephan Kadauke, Richard Hanna, or Ezra Porter for any questions, comments, or concerns.
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This submission for v1.2.2 patches two minor bugs related to data access group handling and labels.
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This submission for v1.2.3 patches two minor bugs related to the clarity of error and warning messages.
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## Test environments
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1. Local macOS Sequoia 15.2, R 4.4.2
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1. Local macOS Sequoia 15.2, R 4.4.0
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2. R-hub
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1. [Ubuntu 24.04.2 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/13978387947/job/39137770004)
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2. [Ubuntu 24.04.2 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/13978387947/job/39137769994)
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3. [Ubuntu 24.04.2 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/13978387947/job/39137770007)
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4. [Microsoft Windows Server 2022, 10.0.20348](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/13978387947/job/39137769995)
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3. [win-builder](https://win-builder.r-project.org/8BK3zt6ki2a4/00check.log), development version.
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1. [Ubuntu 24.04.2 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/15351802286/job/43201633589)
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2. [Ubuntu 24.04.2 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/15351802286/job/43201633580)
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3. [Ubuntu 24.04.2 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/15351802286/job/43201633593)
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4. [Microsoft Windows Server 2022, 10.0.20348](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/15351802286/job/43201633585)
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3. [win-builder](https://win-builder.r-project.org/sXA2nedLAHgM/00check.log), development version.
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4. [GiHub Actions](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions), Ubuntu 20.04.05 LTS
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## R CMD check results:
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- 0 ERRORs or WARNINGs or NOTES on any builds
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- 0 ERRORs or WARNINGs on any builds
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- `win-builder` contained one expected NOTE related to the email address for the `win-builder` submission varying from the package maintainer
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## Downstream Dependencies:
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All packages that depend/import/suggest REDCapTidieR pass the [Reverse dependency checks](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/13978391243).
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All packages that depend/import/suggest REDCapTidieR pass the [Reverse dependency checks](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/15351817999).

‎utility/cli_message_examples_reprex.md

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})
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#> Error:
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#> ✖ File
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#> ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/RtmpQCmzPP/file1411b189a9c52/temp.csv''
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#> ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmpj47vZR/file1866d316efdeb/temp.csv''
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#> already exists.
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#> ℹ Overwriting files is disabled by default. Set `overwrite = TRUE` to overwrite
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#> existing file.
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write_redcap_xlsx(file = filepath)
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})
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#> Warning in write_redcap_xlsx(., file = filepath): ! No extension provided for `file`:
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#> '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/RtmpQCmzPP/file1411b1319086f/temp'
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#> '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmpj47vZR/file1866d20d182be/temp'
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#> ℹ The extension '.xlsx' will be appended to the file name.
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# Printed supertibble

‎utility/microbenchmark_results.csv

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min,lq,mean,median,uq,max,neval,description,source
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0.96,0.96,0.96,0.96,0.96,0.96,1,simple static (read-only) test project,ouhsc
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2.35,2.35,2.35,2.35,2.35,2.35,1,longitudinal (read-only) ARM test project,ouhsc
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0.99,0.99,0.99,0.99,0.99,0.99,1,simple write data,ouhsc
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4.29,4.29,4.29,4.29,4.29,4.29,1,Russian Characters,ouhsc
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6.67,6.67,6.67,6.67,6.67,6.67,1,"super-wide --3,000 columns",ouhsc
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1.72,1.72,1.72,1.72,1.72,1.72,1,static (not longitudinal) survey test project,ouhsc
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1.43,1.43,1.43,1.43,1.43,1.43,1,"Clinical Trial (Fake) --Read-only, contributed by @higgi13425",ouhsc
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1.12,1.12,1.12,1.12,1.12,1.12,1,nonnumeric record_id,ouhsc
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0.97,0.97,0.97,0.97,0.97,0.97,1,DAG Read,ouhsc
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0.9,0.9,0.9,0.9,0.9,0.9,1,potentially problematic values,ouhsc
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1.13,1.13,1.13,1.13,1.13,1.13,1,simple write metadata,ouhsc
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0.89,0.89,0.89,0.89,0.89,0.89,1,DAG Write -admin,ouhsc
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0.95,0.95,0.95,0.95,0.95,0.95,1,DAG Write -group A,ouhsc
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1278.89,1278.89,1278.89,1278.89,1278.89,1278.89,1,"super-wide #3--35,000 columns",ouhsc
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0.99,0.99,0.99,0.99,0.99,0.99,1,Repeating Instruments --Sparse,ouhsc
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1.1,1.1,1.1,1.1,1.1,1.1,1,Delete Single Arm,ouhsc
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2.35,2.35,2.35,2.35,2.35,2.35,1,Delete Multiple Arm,ouhsc
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2.13,2.13,2.13,2.13,2.13,2.13,1,longitudinal single arm,ouhsc
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1.25,1.25,1.25,1.25,1.25,1.25,1,decimal comma and dot,ouhsc
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1.32,1.32,1.32,1.32,1.32,1.32,1,decimal comma,ouhsc
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1.09,1.09,1.09,1.09,1.09,1.09,1,decimal dot,ouhsc
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1.21,1.21,1.21,1.21,1.21,1.21,1,Validation Types,ouhsc
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0.99,0.99,0.99,0.99,0.99,0.99,1,Blank for Gray Status,ouhsc
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1.32,1.32,1.32,1.32,1.32,1.32,1,Checkboxes 1,ouhsc
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1.13,1.13,1.13,1.13,1.13,1.13,1,Vignette: Longitudinal & Repeating Measures,ouhsc
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3.01,3.01,3.01,3.01,3.01,3.01,1,classic,redcaptidier
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3.34,3.34,3.34,3.34,3.34,3.34,1,classic no repeat,redcaptidier
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3.1,3.1,3.1,3.1,3.1,3.1,1,longitudinal,redcaptidier
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2.88,2.88,2.88,2.88,2.88,2.88,1,longitudinal no arms,redcaptidier
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3.5,3.5,3.5,3.5,3.5,3.5,1,longitudinal no repeat,redcaptidier
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5.16,5.16,5.16,5.16,5.16,5.16,1,deep dive vignette,redcaptidier
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2.8,2.8,2.8,2.8,2.8,2.8,1,repeat first instrument,redcaptidier
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4.69,4.69,4.69,4.69,4.69,4.69,1,repeat event,redcaptidier
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2.42,2.42,2.42,2.42,2.42,2.42,1,restricted access,redcaptidier
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1.99,1.99,1.99,1.99,1.99,1.99,1,large sparse db,redcaptidier
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1.63,1.63,1.63,1.63,1.63,1.63,1,data access groups,redcaptidier
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3.62,3.62,3.62,3.62,3.62,3.62,1,longitudinal data access groups,redcaptidier
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3.16,3.16,3.16,3.16,3.16,3.16,1,mixed structure repeat no repeat,redcaptidier
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11.29,11.29,11.29,11.29,11.29,11.29,1,prodigy db,redcaptidier
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15.8,15.8,15.8,15.8,15.8,15.8,1,cart comprehensive db,redcaptidier
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34.07,34.07,34.07,34.07,34.07,34.07,1,bmt outcomes db,redcaptidier
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1.34,1.34,1.34,1.34,1.34,1.34,1,simple static (read-only) test project,ouhsc
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1.89,1.89,1.89,1.89,1.89,1.89,1,longitudinal (read-only) ARM test project,ouhsc
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0.73,0.73,0.73,0.73,0.73,0.73,1,simple write data,ouhsc
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2.38,2.38,2.38,2.38,2.38,2.38,1,Russian Characters,ouhsc
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4.63,4.63,4.63,4.63,4.63,4.63,1,"super-wide --3,000 columns",ouhsc
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1.12,1.12,1.12,1.12,1.12,1.12,1,static (not longitudinal) survey test project,ouhsc
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0.98,0.98,0.98,0.98,0.98,0.98,1,"Clinical Trial (Fake) --Read-only, contributed by @higgi13425",ouhsc
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0.88,0.88,0.88,0.88,0.88,0.88,1,nonnumeric record_id,ouhsc
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0.98,0.98,0.98,0.98,0.98,0.98,1,DAG Read,ouhsc
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0.91,0.91,0.91,0.91,0.91,0.91,1,potentially problematic values,ouhsc
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0.97,0.97,0.97,0.97,0.97,0.97,1,simple write metadata,ouhsc
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0.94,0.94,0.94,0.94,0.94,0.94,1,DAG Write -admin,ouhsc
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0.66,0.66,0.66,0.66,0.66,0.66,1,DAG Write -group A,ouhsc
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149.66,149.66,149.66,149.66,149.66,149.66,1,"super-wide #3--35,000 columns",ouhsc
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0.9,0.9,0.9,0.9,0.9,0.9,1,Repeating Instruments --Sparse,ouhsc
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0.87,0.87,0.87,0.87,0.87,0.87,1,Delete Single Arm,ouhsc
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1.48,1.48,1.48,1.48,1.48,1.48,1,Delete Multiple Arm,ouhsc
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1.67,1.67,1.67,1.67,1.67,1.67,1,longitudinal single arm,ouhsc
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0.91,0.91,0.91,0.91,0.91,0.91,1,decimal comma and dot,ouhsc
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0.9,0.9,0.9,0.9,0.9,0.9,1,decimal comma,ouhsc
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0.9,0.9,0.9,0.9,0.9,0.9,1,decimal dot,ouhsc
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1.03,1.03,1.03,1.03,1.03,1.03,1,Validation Types,ouhsc
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1.07,1.07,1.07,1.07,1.07,1.07,1,Blank for Gray Status,ouhsc
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0.86,0.86,0.86,0.86,0.86,0.86,1,Checkboxes 1,ouhsc
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1.04,1.04,1.04,1.04,1.04,1.04,1,Vignette: Longitudinal & Repeating Measures,ouhsc
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1.32,1.32,1.32,1.32,1.32,1.32,1,classic,redcaptidier
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2.07,2.07,2.07,2.07,2.07,2.07,1,classic no repeat,redcaptidier
29+
2.35,2.35,2.35,2.35,2.35,2.35,1,longitudinal,redcaptidier
30+
2.35,2.35,2.35,2.35,2.35,2.35,1,longitudinal no arms,redcaptidier
31+
4.16,4.16,4.16,4.16,4.16,4.16,1,longitudinal no repeat,redcaptidier
32+
2.72,2.72,2.72,2.72,2.72,2.72,1,deep dive vignette,redcaptidier
33+
1.18,1.18,1.18,1.18,1.18,1.18,1,repeat first instrument,redcaptidier
34+
2.31,2.31,2.31,2.31,2.31,2.31,1,repeat event,redcaptidier
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1.23,1.23,1.23,1.23,1.23,1.23,1,restricted access,redcaptidier
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1.36,1.36,1.36,1.36,1.36,1.36,1,large sparse db,redcaptidier
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1.22,1.22,1.22,1.22,1.22,1.22,1,data access groups,redcaptidier
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2.31,2.31,2.31,2.31,2.31,2.31,1,longitudinal data access groups,redcaptidier
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2.38,2.38,2.38,2.38,2.38,2.38,1,mixed structure repeat no repeat,redcaptidier
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8.12,8.12,8.12,8.12,8.12,8.12,1,prodigy db,redcaptidier
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6.22,6.22,6.22,6.22,6.22,6.22,1,cart comprehensive db,redcaptidier

‎utility/refresh.R

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@@ -64,8 +64,11 @@ devtools::check( # Equivalent of R-hub
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incoming = TRUE
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)
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# Approx matches to https://cran.r-project.org/web/checks/check_flavors.html
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rhub::rhub_check(platforms = c("linux", "windows", "ubuntu-next", "ubuntu-release")) # These will be available in GitHub Actions
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devtools::check_win_devel(email = "hannar1@chop.edu") # CRAN submission policies encourage the development version
67+
rhub::rhub_check(
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platforms = c("linux", "windows", "ubuntu-next", "ubuntu-release"),
69+
gh_url = "https://github.com/CHOP-CGTInformatics/REDCapTidieR"
70+
) # These will be available in GitHub Actions
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devtools::check_win_devel(email = "porterej@chop.edu") # CRAN submission policies encourage the development version
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# Note: Must be off of VPN
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# To run reverse dependency check, manually trigger the "Revere dependency check" workflow in GitHub Actions
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# Careful, the last question ultimately uploads it to CRAN, where you can't delete/reverse your decision.

‎utility/test_creds.R

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microbenchmark_fx <- function(redcap_uri, token, name, times = 1){
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microbenchmark(
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name = suppressWarnings(read_redcap(redcap_uri = redcap_uri, token = token, allow_mixed_structure = TRUE)),
47+
name = suppressWarnings(read_redcap(
48+
redcap_uri = redcap_uri,
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token = token,
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allow_mixed_structure = TRUE,
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export_data_access_groups = FALSE
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)
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),
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times = times,
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unit = "seconds"
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)

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