CRAN 1.2 preparation

CHOP-CGTInformatics · Oct 23, 2024 · 335ecc9 · 335ecc9
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diff --git a/README.Rmd b/README.Rmd
@@ -25,7 +25,7 @@ knitr::opts_chunk$set(
 [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/6845/badge)](https://bestpractices.coreinfrastructure.org/projects/6845)
 <!-- badges: end -->
 
-The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) data from a [REDCap](https://www.project-redcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the [REDCap API](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#redcap-api) and then transforms the returned data into a set of [tidy](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tidy) [tibbles](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tibble).
+The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) data from a [REDCap](https://projectredcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the [REDCap API](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#redcap-api) and then transforms the returned data into a set of [tidy](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tidy) [tibbles](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tibble).
 
 REDCapTidieR is especially useful for dealing with complex REDCap projects that are [longitudinal](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#longitudinal-project) or include [repeating](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#repeating) [instruments](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#instrument) or both.
 

diff --git a/README.md b/README.md
@@ -16,12 +16,11 @@ status](https://www.r-pkg.org/badges/version/REDCapTidieR)](https://CRAN.R-proje
 coverage](https://codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR?branch=main)
 [![OpenSSF Best
 Practices](https://bestpractices.coreinfrastructure.org/projects/6845/badge)](https://bestpractices.coreinfrastructure.org/projects/6845)
-[![DOI](https://joss.theoj.org/papers/10.21105/joss.06277/status.svg)](https://doi.org/10.21105/joss.06277)
 <!-- badges: end -->
 
 The REDCapTidieR package provides an elegant way to
 [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import)
-data from a [REDCap](https://www.project-redcap.org/)
+data from a [REDCap](https://projectredcap.org/)
 [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project)
 into an R environment. It builds upon the
 [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the

diff --git a/cran-comments.md b/cran-comments.md
@@ -6,23 +6,23 @@ This submission for v1.2.0 adds new functionality, new documentation, and patche
 
 ## New Features
 
-The only new feature in this release in is an analytics function that exists in a silo away from the rest of the core package.
+The only new feature in this release is an analytics function that exists in a silo away from the rest of the core package.
 
 ## Test environments
 
-1. Local macOS Sonoma 14.6.1, R 4.4.0
-2. R-hub
-    1. [Ubuntu 22.04.5 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634537921)
-    2. [Ubuntu 22.04.5 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634538851)
-    3. [Ubuntu 22.04.4 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634538452)
-    4. [Microsoft Windows Server 2022, 10.0.20348](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11371750216/job/31634539238)
-3.  [win-builder](https://win-builder.r-project.org/zPkjljy8Z67c/), development version.
+1.  Local macOS Sonoma 14.6.1, R 4.4.0
+2.  R-hub
+    1.  [Ubuntu 22.04.5 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969845126)
+    2.  [Ubuntu 22.04.5 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969845814)
+    3.  [Ubuntu 22.04.4 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969845504)
+    4.  [Microsoft Windows Server 2022, 10.0.20348](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969846106)
+3.  [win-builder](https://win-builder.r-project.org/OQCea7cbW815/), development version.
 4.  [GiHub Actions](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions), Ubuntu 20.04.05 LTS
 
 ## R CMD check results:
 
-- 0 ERRORs or WARNINGs on any builds
+-   0 ERRORs or WARNINGs on any builds
 
 ## Downstream Dependencies:
 
-
+All packages that depend/import/suggest REDCapTidieR pass the [Reverse dependency checks](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486797194).
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -54,7 +54,7 @@ @Manual{redcapr_cit
   author = {Will Beasley},
   year = {2023},
   url = {https://ouhscbbmc.github.io/REDCapR/},
-  note = {https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://project-redcap.org},
+  note = {https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org},
 }
 
 @Manual{redcapapi_cit,

diff --git a/paper/paper.html b/paper/paper.html
@@ -381,7 +381,7 @@ <h4 class="date">XX November 2023</h4>
 <div id="summary" class="section level1">
 <h1>Summary</h1>
 <p>Capturing and storing electronic data is integral in the research
-world. <a href="https://www.project-redcap.org/">REDCap</a> <span class="citation">(Harris et al. 2009, 2019)</span> offers a secure web
+world. <a href="https://projectredcap.org/">REDCap</a> <span class="citation">(Harris et al. 2009, 2019)</span> offers a secure web
 application that lets users build databases and surveys with a robust
 front-end interface that can support data of any type, including data
 requiring compliance with standards for protected information.</p>

diff --git a/paper/paper.md b/paper/paper.md
@@ -48,7 +48,7 @@ bibliography: paper.bib
 
 # Summary
 
-Capturing and storing electronic data is integral in the research world. [REDCap](https://www.project-redcap.org/) [@Harris2009; @Harris2019] offers a secure web application that lets users build databases and surveys with a robust front-end interface that can support data of any type, including data requiring compliance with standards for protected information.
+Capturing and storing electronic data is integral in the research world. [REDCap](https://projectredcap.org/) [@Harris2009; @Harris2019] offers a secure web application that lets users build databases and surveys with a robust front-end interface that can support data of any type, including data requiring compliance with standards for protected information.
 
 Many REDCap users use the R programming language [@r_cit] to extract and analyze their data. The [`REDCapR`](https://cran.r-project.org/web/packages/REDCapR/index.html) [@redcapr_cit] and [`redcapAPI`](https://cran.r-project.org/web/packages/redcapAPI/index.html) [@redcapapi_cit] packages allow R users to extract data directly into their programming environment. While this works well for simple REDCap databases, it becomes cumbersome for complex databases, because the REDCap API outputs a "block matrix"--a single table with varied granularity levels, which conflicts with the "tidy data" framework [@Wickham2014] that advocates for standardized data organization.
 

diff --git a/utility/refresh.R b/utility/refresh.R
@@ -65,7 +65,7 @@ devtools::check( # Equivalent of R-hub
 )
 # Approx matches to https://cran.r-project.org/web/checks/check_flavors.html
 rhub::rhub_check(platforms = c("linux", "windows", "ubuntu-next", "ubuntu-release")) # These will be available in GitHub Actions
-devtools::check_win_devel(email = "porterej@chop.edu") # CRAN submission policies encourage the development version
+devtools::check_win_devel(email = "hannar1@chop.edu") # CRAN submission policies encourage the development version
 # Note: Must be off of VPN
 # To run reverse dependency check, manually trigger the "Revere dependency check" workflow in GitHub Actions
 # Careful, the last question ultimately uploads it to CRAN, where you can't delete/reverse your decision.

diff --git a/vignettes/REDCapTidieR.Rmd b/vignettes/REDCapTidieR.Rmd
@@ -26,7 +26,7 @@ redcap_uri <- Sys.getenv("REDCAP_URI")
 token <- Sys.getenv("SUPERHEROES_REDCAP_API")
 ```
 
-[REDCap](https://www.project-redcap.org/) is an electronic data capture software that is widely used in the academic research community. The [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package streamlines calls to the REDCap API from an R environment. One of REDCapR's main uses is to [import](glossary.html#import) [records](glossary.html#record) from a REDCap [project](glossary.html#project). This works well for simple projects, however becomes ugly when complex databases that include [longitudinal](glossary.html#longitudinal-project) structure and/or [repeating](glossary.html#repeating) [instruments](glossary.html#instrument) are involved.
+[REDCap](https://projectredcap.org/) is an electronic data capture software that is widely used in the academic research community. The [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package streamlines calls to the REDCap API from an R environment. One of REDCapR's main uses is to [import](glossary.html#import) [records](glossary.html#record) from a REDCap [project](glossary.html#project). This works well for simple projects, however becomes ugly when complex databases that include [longitudinal](glossary.html#longitudinal-project) structure and/or [repeating](glossary.html#repeating) [instruments](glossary.html#instrument) are involved.
 
 The REDCapTidieR package aims to make the life of analysts who deal with complex REDCap databases easier. It builds upon **REDCapR** to make its output **tidier**. Instead of [one large data frame that contains all the data from your project](glossary.html#block-matrix), you get to work with a set of [tidy](glossary.html#tidy) [tibbles](glossary.html#tibble), one for each REDCap [instrument](glossary.html#instrument).