Merge pull request #404 from OuhscBbmc/dev

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OuhscBbmc · Aug 10, 2022 · efd8a74 · efd8a74
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -25,3 +25,4 @@ utility/
 ^codecov\.yml$
 ^pkgdown$
 ^LICENSE\.md$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,7 @@ Description: Encapsulates functions to streamline calls from R to the REDCap
     University.  The Application Programming Interface (API) offers an avenue
     to access and modify data programmatically, improving the capacity for
     literate and reproducible programming.
-Version: 1.0.9002
+Version: 1.1.0
 Authors@R: c(person("Will", "Beasley", role = c("aut", "cre"), email =
     "[email protected]", comment = c(ORCID = "0000-0002-5613-5006")),
     person("David", "Bard", role = "ctb"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-Upcoming Versions
+Version 1.1.0 (released 2022-08-10)
 ==========================================================
 
 ### New Features
@@ -41,7 +41,7 @@ The package has been stable for years and should be reflected in the major versi
 * The functions `redcap_read_oneshot()`, `redcap_read()`, & `redcap_read_oneshot_eav()` now support the parameters `datetime_range_begin` and `datetime_range_end`.  The are passed to the REDCap parameters `dateRangeBegin` and `dateRangeEnd`, which restricts records returned, based on their last modified date in the server.  (Thanks @pbchase, #321 & #323.)
 * Better documentation about the `export_survey_fields` parameter in the functions `redcap_read()` & `redcap_read_oneshot()`.  (Thanks @isaactpetersen, #333)
 * New function [`redcap_report()`](https://ouhscbbmc.github.io/REDCapR/reference/redcap_report.html) export records that populate a REDCap report. (#326.)
-* New vignette [Typical REDCap Workflow for a Data Analyst](https://ouhscbbmc.github.io/REDCapR/articles/workflow-read.html) developed to support a workshop for the 2021 [R/Medicine Conference](https://r-medicine.org/) (#332, with  @higgi13425, @kamclean, & Amanda Miller)
+* New vignette [Typical REDCap Workflow for a Data Analyst](https://ouhscbbmc.github.io/REDCapR/articles/workflow-read.html) developed to support a workshop for the 2021 [R/Medicine Conference](https://events.linuxfoundation.org/r-medicine/) (#332, with  @higgi13425, @kamclean, & Amanda Miller)
 * New function [`create_credential_local()`](https://ouhscbbmc.github.io/REDCapR/reference/retrieve_credential.html) starts a well-formed csv file that can contain tokens. (#340, after conversations with @higgi13425 & @kamclean.)
 
 ### Stability Features
@@ -267,8 +267,9 @@ Version 0.1 (Released 2014-01-14)
 * `redcap_read()` takes parameter for `raw_or_label` (Thanks Rollie Parrish #3)
 * `redcap_read()` takes parameter for `export_data_access_groups` thanks to Rollie Parrish (@rparrish #4)
 
+----------------------------------------
+
 GitHub Commits and Releases
-==========================================================
 
-* For a detailed change log, please see https://github.com/OuhscBbmc/REDCapR/commits/master.
+* For a detailed change log, please see https://github.com/OuhscBbmc/REDCapR/commits/main.
 * For a list of the major releases, please see https://github.com/OuhscBbmc/REDCapR/releases.
diff --git a/R/REDCapR-package.R b/R/REDCapR-package.R
@@ -28,7 +28,7 @@
 #' collaboration with [OKDHS](https://oklahoma.gov/okdhs.html);
 #' David Bard, PI, OUHSC; 2014-2017.
 #' * *Integrative Analysis of Longitudinal Studies of Aging (IALSA)*,
-#' sponsored by [NIH 5P01AG043362](https://grantome.com/grant/NIH/P01-AG043362).
+#' sponsored by [NIH 5P01AG043362](https://grantome.com/grant/NIH/P01-AG043362-05).
 #' Scott Hofer, PI, University of Victoria;
 #' Will Beasley, PI of site-award, OUHSC; 2013-2018.
 #' * *Oklahoma Shared Clinical and Translational Resources*, sponsored by

diff --git a/R/constant.R b/R/constant.R
@@ -47,7 +47,7 @@
 #' To add more, please for and edit
 #' [constant.R](https://github.com/OuhscBbmc/REDCapR/blob/master/R/constant.R)
 #' on GitHub and submit a pull request.  For instructions, please see
-#' [Editing files in another user's repository](https://help.github.com/articles/editing-files-in-another-user-s-repository/) # nolint
+#' [Editing files in another user's repository](https://docs.github.com/articles/editing-files-in-another-user-s-repository/) # nolint
 #' in the GitHub documentation.
 #'
 #' @author Will Beasley

diff --git a/R/redcap-read-oneshot.R b/R/redcap-read-oneshot.R
@@ -101,7 +101,7 @@
 #' If you do not pass in this `export_data_access_groups` value, it will default
 #' to `FALSE`. The following is from the API help page for version 10.5.1:
 #' *This flag is only viable if the user whose token is being used to make the
-#' API request is *not* in a data access group. If the user is in a group,
+#' API request is **not** in a data access group. If the user is in a group,
 #' then this flag will revert to its default value*.
 #'
 #' @author Will Beasley

diff --git a/README.md b/README.md
@@ -58,7 +58,7 @@ We'd like to thank the following developers for their [advice](https://github.co
 
 ### Funders
 
-Much of this package has been developed to support the needs of the following projects.  We appreciate the support.  (So far) the primary developers of REDCapR are the external evaluators for [Oklahoma's MIECHV](https://oklahoma.gov/health/family-health/family-support-and-prevention-service.html) program.  See the preliminary CQI reports (many of which use REDCapR) at https://ouhscbbmc.github.io/MReportingPublic/.
+Much of this package has been developed to support the needs of the following projects.  We appreciate the support.  (So far) the primary developers of REDCapR are the external evaluators for [Oklahoma's MIECHV](https://oklahoma.gov/health/health-education/children---family-health/family-support-and-prevention-service/miechv-program-federal-home-visiting-grant.html) program.  See the preliminary CQI reports (many of which use REDCapR) at https://ouhscbbmc.github.io/MReportingPublic/.
 
 * *OUHSC CCAN Independent Evaluation of the State of Oklahoma Competitive Maternal, Infant, and Early Childhood Home Visiting ([MIECHV](https://mchb.hrsa.gov/maternal-child-health-initiatives/home-visiting-overview)) Project*. HRSA/ACF D89MC23154.  David Bard, PI, OUHSC; 2011-2015.
 * *Independent Evaluation of the State of OK MIECHV Evidence Based Home Visitation Project*, [NIH](https://www.nih.gov/)-sponsored collaboration with [OSDH](https://oklahoma.gov/health.html). David Bard, PI, OUHSC; 2015-2017.

diff --git a/REDCapR.Rproj b/REDCapR.Rproj
@@ -17,6 +17,5 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageCleanBeforeInstall: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace,vignette
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -49,6 +49,7 @@ reference:
       Accessing other information from the REDCap project or server.
     contents:
       - redcap_arm_export
+      - redcap_dag_read
       - redcap_delete
       - redcap_download_instrument
       - redcap_event_instruments

diff --git a/cran-comments.md b/cran-comments.md
@@ -10,29 +10,47 @@ Thank you for taking the time to review my submission, and please tell me if the
 Test environments
 -----------------------------------------------
 
-1. Local Ubuntu, R 4.1.2 patched
-1. Local Win8, R 4.1.2 patched
-1. Local Win10, R 4.1.2 patched
+1. Local Ubuntu, R 4.2.1 patched
+1. Local Win10, R 4.2.1 patched
 1. R-hub
-    1. [Ubuntu Linux 20.04 LTS, R-release, GCC](https://builder.r-hub.io/status/REDCapR_1.0.0.tar.gz-d554cfab8fed4acba83ca159d2a14a7b)
-    1. [Fedora Linux, R-devel, clang, gfortran](https://builder.r-hub.io/status/REDCapR_1.0.0.tar.gz-80a6d6b66bb84847b61d31f6029f5628)
-    1. [Windows Server](https://builder.r-hub.io/status/REDCapR_1.0.0.tar.gz-b5b0cb95fb4746f9b354071b89caaafa)
-1. [win-builder](https://win-builder.r-project.org/BwNz2bnHxuse), development version.
+    1. [Ubuntu Linux 20.04 LTS, R-release, GCC](https://builder.r-hub.io/status/REDCapR_1.1.0.tar.gz-65720cf9ae694996b81294e2ade39175)
+    1. [Fedora Linux, R-devel, clang, gfortran](https://builder.r-hub.io/status/REDCapR_1.1.0.tar.gz-dfbf2b851e0c48aeaaf8e85c9c34c332)
+    1. [Windows Server](https://builder.r-hub.io/status/REDCapR_1.1.0.tar.gz-6fe170ebb60e41469336c822ca3465da)
+1. [win-builder](https://win-builder.r-project.org/h66QMt5KzueV), development version.
 1. [GiHub Actions](https://github.com/OuhscBbmc/REDCapR/actions), Ubuntu 20.04 LTS
 
 R CMD check results
 -----------------------------------------------
 
 * No ERRORs or WARNINGs on any builds.
-  * One ignorable exception:  the win-builder and Windows Server R-hub builds don't yet have the newest version of readr.  I see they're using readr 1.4.0 and returns the error "Package required and available but unsuitable version: 'readr'".  But it runs well on my two local Windows machines.
-  * A second ignorable exception: R-hub refers to Bioconductor, which REDCapR doesn't use: "Error : Bioconductor does not yet build and check packages for R version 4.2;"
 
-* A NOTE is returned for the Zenodo.org URL being possibly invalid.  It resolves in a browser, but is takes a while; I'm guessing their website's slow today.
+* A NOTE is returned for a few websites.  All are accessible by browser.
+  * https://grantome.com/grant/NIH/P01-AG043362
+  * https://grantome.com/grant/NIH/U54-GM104938
+  * https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=U54GM104938&arg_ProgOfficeCode=127
+  * https://www.researchgate.net/profile/William-Beasley-5
+
+* There is one NOTE that is only found on R-hub Windows (Server 2022, R-devel 64-bit):
+
+  ```txt
+  * checking for detritus in the temp directory ... NOTE
+  Found the following files/directories:
+    'lastMiKTeXException'
+  As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this could be due to a bug/crash in MiKTeX and can likely be ignored.
+  ```
+
+* There is one NOTE that is only found on the R-hub Fedora:
+
+  ```txt
+  * checking HTML version of manual ... NOTE
+  Skipping checking HTML validation: no command 'tidy' found
+  ```
+
+  Based on [this discussion](https://groups.google.com/g/r-sig-mac/c/7u_ivEj4zhM?pli=1), it sounds like a problem with the testing environment, and not the package code.
 
 Downstream dependencies
 -----------------------------------------------
 
-No downstream pakcages are affected.  The two packages that depends/imports/suggests REDCapR passes checks with `revdepcheck::revdep_check()`.  Results: https://github.com/OuhscBbmc/REDCapR/blob/master/revdep/cran.md
-
-    * [codified](https://CRAN.R-project.org/package=codified)
-    * [ReviewR](https://CRAN.R-project.org/package=ReviewR)
+No downstream packages are affected.  The package that depends/imports/suggests REDCapR passes checks with `revdepcheck::revdep_check()`.  Results: https://github.com/OuhscBbmc/REDCapR/blob/main/revdep/cran.md
+
+* [ReviewR](https://CRAN.R-project.org/package=ReviewR)
diff --git a/man/REDCapR-package.Rd b/man/REDCapR-package.Rd
diff --git a/man/constant.Rd b/man/constant.Rd
diff --git a/man/redcap_read_oneshot.Rd b/man/redcap_read_oneshot.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,61 +1,2 @@
 # Platform
 
-|field    |value                                       |
-|:--------|:-------------------------------------------|
-|version  |R version 4.1.0 Patched (2021-05-29 r80415) |
-|os       |Windows >= 8 x64                            |
-|system   |x86_64, mingw32                             |
-|ui       |RStudio                                     |
-|language |(EN)                                        |
-|collate  |English_United States.1252                  |
-|ctype    |English_United States.1252                  |
-|tz       |America/Chicago                             |
-|date     |2021-07-21                                  |
-
-# Dependencies
-
-|package     |old    |new     |<U+0394>  |
-|:-----------|:------|:-------|:--|
-|REDCapR     |0.11.0 |1.0.0.0 |*  |
-|askpass     |1.1    |1.1     |   |
-|backports   |1.2.1  |1.2.1   |   |
-|bit         |4.0.4  |4.0.4   |   |
-|bit64       |4.0.5  |4.0.5   |   |
-|checkmate   |2.0.0  |2.0.0   |   |
-|cli         |3.0.1  |3.0.1   |   |
-|clipr       |0.7.1  |0.7.1   |   |
-|cpp11       |0.3.1  |0.3.1   |   |
-|crayon      |1.4.1  |1.4.1   |   |
-|curl        |4.3.2  |4.3.2   |   |
-|dplyr       |1.0.7  |1.0.7   |   |
-|ellipsis    |0.3.2  |0.3.2   |   |
-|fansi       |0.5.0  |0.5.0   |   |
-|generics    |0.1.0  |0.1.0   |   |
-|glue        |1.4.2  |1.4.2   |   |
-|hms         |1.1.0  |1.1.0   |   |
-|httr        |1.4.2  |1.4.2   |   |
-|jsonlite    |1.7.2  |1.7.2   |   |
-|lifecycle   |1.0.0  |1.0.0   |   |
-|magrittr    |2.0.1  |2.0.1   |   |
-|mime        |0.11   |0.11    |   |
-|openssl     |1.4.4  |1.4.4   |   |
-|pillar      |1.6.1  |1.6.1   |   |
-|pkgconfig   |2.0.3  |2.0.3   |   |
-|prettyunits |1.1.1  |1.1.1   |   |
-|progress    |1.2.2  |1.2.2   |   |
-|purrr       |0.3.4  |0.3.4   |   |
-|R6          |2.5.0  |2.5.0   |   |
-|readr       |2.0.0  |2.0.0   |   |
-|rlang       |0.4.11 |0.4.11  |   |
-|sys         |3.4    |3.4     |   |
-|tibble      |3.1.2  |3.1.2   |   |
-|tidyr       |1.1.3  |1.1.3   |   |
-|tidyselect  |1.1.1  |1.1.1   |   |
-|tzdb        |0.1.2  |0.1.2   |   |
-|utf8        |1.2.1  |1.2.1   |   |
-|vctrs       |0.3.8  |0.3.8   |   |
-|vroom       |1.5.3  |1.5.3   |   |
-|withr       |2.4.2  |2.4.2   |   |
-
-# Revdeps
-
diff --git a/vignettes/BasicREDCapROperations.Rmd b/vignettes/BasicREDCapROperations.Rmd
@@ -27,7 +27,7 @@ opts_chunk$set(
   tidy    = FALSE
 )
 
-knit_print.data.frame = function(x, ...) {
+knit_print.data.frame <- function(x, ...) {
   # See https://cran.r-project.org/package=knitr/vignettes/knit_print.html
   # res = paste(c("", "", kable(x)), collapse = "\n")
   # asis_output(res)

diff --git a/vignettes/advanced-redcapr-operations.Rmd b/vignettes/advanced-redcapr-operations.Rmd
@@ -26,7 +26,7 @@ opts_chunk$set(
 )
 
 # knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
-knit_print.data.frame = function(x, ...) {
+knit_print.data.frame <- function(x, ...) {
   # See https://cran.r-project.org/package=knitr/vignettes/knit_print.html
 
   x %>%
@@ -70,7 +70,7 @@ Converting from tall/long to wide
 However we like going wide to produce visual tables for publications, and here's one way to do it in R. First retrieve the dataset from REDCap.
 
 ```{r retrieve-longitudinal, results='hold'}
-library(magrittr);
+library(magrittr)
 suppressPackageStartupMessages(requireNamespace("dplyr"))
 suppressPackageStartupMessages(requireNamespace("tidyr"))
 events_to_retain  <- c("dose_1_arm_1", "visit_1_arm_1", "dose_2_arm_1", "visit_2_arm_1")

diff --git a/vignettes/workflow-read.Rmd b/vignettes/workflow-read.Rmd
@@ -290,7 +290,7 @@ https://github.com/OuhscBbmc/RedcapExamplesAndPatterns/blob/master/Publications/
 Downstream Reproducible Reports
 -------------------------
 
-Once the dataset is in R, take advantage of all the reproducible research tools available.  Tomorrow, [R/Medicine](https://r-medicine.org/) has a workshop on this topic using the exciting new [Quarto](https://quarto.org/) program that's similar to R Markdown.  Also see the relevant [R/Medicine 2020 presentation videos](https://www.youtube.com/playlist?list=PL4IzsxWztPdljYo7uE5G_R2PtYw3fUReo).  And of course, [any book by Yihui Xie and colleagues](https://www.amazon.com/Yihui-Xie/e/B00E9CQJGY?ref=sr_ntt_srch_lnk_1&qid=1625895927&sr=1-1).
+Once the dataset is in R, take advantage of all the reproducible research tools available.  Tomorrow, [R/Medicine](https://events.linuxfoundation.org/r-medicine/) has a workshop on this topic using the exciting new [Quarto](https://quarto.org/) program that's similar to R Markdown.  Also see the relevant [R/Medicine 2020 presentation videos](https://www.youtube.com/playlist?list=PL4IzsxWztPdljYo7uE5G_R2PtYw3fUReo).  And of course, [any book by Yihui Xie and colleagues](https://www.amazon.com/Yihui-Xie/e/B00E9CQJGY?ref=sr_ntt_srch_lnk_1&qid=1625895927&sr=1-1).
 
 
 Batching
@@ -308,4 +308,4 @@ Notes
 
 This vignette was originally designed for a 2021 R/Medicine REDCap workshop with [Peter Higgins](https://www.med.umich.edu/higginslab/), [Amanda Miller](https://coloradosph.cuanschutz.edu/resources/directory/directory-profile/Miller-Amanda-UCD6000053152), and [Kenneth McLean](https://twitter.com/kennethmclean92).
 
-This work was made possible in part by the NIH grant [U54GM104938](https://hsrproject.nlm.nih.gov/view_hsrproj_record/20204379) to the [Oklahoma Shared Clinical and Translational Resource)](http://osctr.ouhsc.edu).
+This work was made possible in part by the NIH grant [U54GM104938](https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=U54GM104938&arg_ProgOfficeCode=127) to the [Oklahoma Shared Clinical and Translational Resource)](http://osctr.ouhsc.edu).