Merge pull request #8 from OuhscBbmc/dev

Dev
OuhscBbmc · Sep 7, 2018 · c2fa696 · c2fa696
2 parents de95a94 + eb3e35d
commit c2fa696
Show file tree

Hide file tree

Showing 22 changed files with 773 additions and 1,339 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: codified
-Title: Produce standard/formalized demographics tables
+Title: Produce Standard/Formalized Demographics Tables
 Description: Augment clinical data with metadata to create
     output used in conventional publications and reports.
-Version: 0.1.1.9001
-Date: 2018-08-27
+Version: 0.2.0
+Date: 2018-09-06
 Authors@R: c(person("Will", "Beasley", role = c("aut", "cre"), email =
     "wibeasley@hotmail.com", comment = c(ORCID = "0000-0002-5613-5006")),
     person("Peter", "Higgins", role = "ctb"))
@@ -13,24 +13,21 @@ Depends:
     R(>= 3.0.0),
     stats
 Imports:
+    checkmate (>= 1.8.4),
     dplyr (>= 0.7.0),
+    kableExtra,
+    knitr (>= 1.18.0),
     magrittr,
     methods,
-    readr (>= 1.2.0),
+    readr (>= 1.1.0),
     rlang,
     tibble (>= 1.4.0),
     tidyr (>= 0.7.0)
 Suggests:
-    checkmate  (>= 1.8.4),
     devtools,
-    kableExtra,
-    knitr (>= 1.18.0),
     REDCapR,
     rmarkdown,
-    sessioninfo,
-    testthat (>= 0.9)
-Remotes:
-  github::tidyverse/readr
+    testthat (>= 2.0)
 License: MIT + file LICENSE
 LazyData: TRUE
 VignetteBuilder: knitr

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
-# codified 0.0.1.9001
 
-* Added a `NEWS.md` file to track changes to the package.
+# codified 0.2.0
+
+* added `table_nih_enrollment()` and `table_nih_enrollment_pretty()`. #2
+* added `nih-enrollment-html` vignette. #6
+* started pkgdown site. #7
+* the idea was created by [Peter Higgins](http://www.med.umich.edu/higginslab/) (@higgi13425) for [R/Medicine 2018](http://r-medicine.com/).
diff --git a/R/table-nih-enrollment.R b/R/table-nih-enrollment.R
@@ -1,7 +1,7 @@
 #' @name table_nih_enrollment
 #' @aliases  table_nih_enrollment table_nih_enrollment_pretty
 #'
-#' @title Produce an NIH-compliant enrolment table.
+#' @title Produce an NIH-compliant enrollment table.
 #'
 #' @description Produce an NIH enrollment table, leveraging metadata to adapt to the observed [data.frame].
 #'

diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ devtools::install_github(repo="OuhscBbmc/codified")
 
 In the future, the *release* version can be installed from [CRAN](https://cran.r-project.org/package=codified).
 ```r
-# install.packages("codified") # Not yet on CRAN.
+install.packages("codified")
 ```
 
 The package can be uninstalled from your local machine with `remove.packages("codified")`.

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,31 @@
+Description
+-----------------------------------------------
+This is a new release.
+
+Thank you for taking the time to review my submission, and please tell me if there's something else I should do for CRAN.  -Will Beasley
+
+
+Test environments
+-----------------------------------------------
+
+The win-builder and a local machine have used the CRAN version of dplyr.  The others have used the current GitHub master version of dplyr.
+
+* Local Ubuntu, R 3.5.1 patched
+* [win-builder](https://win-builder.r-project.org/9fyA0Vz5XQNU/) (version="R-devel")
+* [Travis CI](https://travis-ci.org/OuhscBbmc/codified), Ubuntu LTS
+* [AppVeyor](https://ci.appveyor.com/project/wibeasley/codified), Windows Server
+
+
+R CMD check results
+-----------------------------------------------
+
+* No ERRORs or WARNINGs on any builds.
+
+* No NOTEs other than 'New submission'
+
+
+Downstream dependencies
+-----------------------------------------------
+
+No other packages depend/import this one.
+
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/nih-enrollment-html.html b/docs/articles/nih-enrollment-html.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/codified-package.html b/docs/reference/codified-package.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/table_nih_enrollment.html b/docs/reference/table_nih_enrollment.html
diff --git a/documentation-for-developers/refresh.R b/documentation-for-developers/refresh.R
@@ -16,3 +16,8 @@ test_results_checked <- devtools::test()
 test_results_checked <- devtools::test(filter = "table-nih-enrollment")
 # testthat::test_dir("./tests/")
 test_results_not_checked <- testthat::test_dir("./tests/manual/")
+
+# devtools::check(force_suggests = FALSE)
+# devtools::build_win(version="R-devel") #CRAN submission policies encourage the development version
+# devtools::revdep_check(pkg="codified", recursive=TRUE)
+# devtools::release(check=FALSE) #Careful, the last question ultimately uploads it to CRAN, where you can't delete/reverse your decision.
diff --git a/inst/doc/nih-enrollment-html.R b/inst/doc/nih-enrollment-html.R
@@ -84,11 +84,26 @@ if( !requireNamespace("REDCapR", quietly=T) )
 library(REDCapR)
 
 ## ----redcap-establish----------------------------------------------------
-ds_2 <- REDCapR::redcap_read_oneshot(
-  redcap_uri = "https://bbmc.ouhsc.edu/redcap/api/",  # URL of REDCap Server.
-  token      = "F304DEC3793FECC3B6DEEFF66302CAD3",    # User-speciifc token/password.
-  guess_type = FALSE                                  # Keep all variables as strings/characters.
-)$data
+if( !requireNamespace("REDCapR", quietly=TRUE) ) {
+  ds <- ds_2 # If REDCapR isn't installed, use the previous version of the dataset.
+} else if( "0.9.8" < packageVersion("REDCapR") ) {
+  ds_2 <- REDCapR::redcap_read_oneshot(
+    redcap_uri = "https://bbmc.ouhsc.edu/redcap/api/",  # URL of REDCap Server.
+    token      = "F304DEC3793FECC3B6DEEFF66302CAD3",    # User-specific token/password.
+    guess_type = FALSE                                  # Keep all variables as strings/characters.
+  )$data  
+} else {
+  # Older versions of REDCapR don't have the `guess_type` parameter
+  ds_2 <- REDCapR::redcap_read_oneshot(
+    redcap_uri = "https://bbmc.ouhsc.edu/redcap/api/",  # URL of REDCap Server.
+    token      = "F304DEC3793FECC3B6DEEFF66302CAD3"     # User-specific token/password.
+  )$data %>% 
+    dplyr::mutate(
+      gender      = as.character(gender),
+      race        = as.character(race),
+      ethnicity   = as.character(ethnicity)
+    )
+}
 
 ## ----redcap-local-cosmetically-format------------------------------------
 table_nih_enrollment_pretty(
@@ -129,4 +144,3 @@ table_nih_enrollment_pretty(
   d_lu_race       = ds_lu_race_3
 )
 
-
diff --git a/inst/doc/nih-enrollment-html.Rmd b/inst/doc/nih-enrollment-html.Rmd
@@ -135,14 +135,38 @@ if( !requireNamespace("REDCapR", quietly=T) )
 library(REDCapR)
 ```
 
-Next, download the data from the REDCap database into the `ds_2` data.frame.
+Next, download the data from the REDCap database into the `ds_2` data.frame.  If you're running the most recent version of REDCapR (available on GitHub), the code will be:
 
-```{r redcap-establish}
+```r
 ds_2 <- REDCapR::redcap_read_oneshot(
   redcap_uri = "https://bbmc.ouhsc.edu/redcap/api/",  # URL of REDCap Server.
-  token      = "F304DEC3793FECC3B6DEEFF66302CAD3",    # User-speciifc token/password.
+  token      = "F304DEC3793FECC3B6DEEFF66302CAD3",    # User-specific token/password.
   guess_type = FALSE                                  # Keep all variables as strings/characters.
-)$data
+)$data  
+```
+The following code is more complicated than normal, because the vignette has to account for different versions of REDCapR being installed on the machine.
+
+```{r redcap-establish}
+if( !requireNamespace("REDCapR", quietly=TRUE) ) {
+  ds <- ds_2 # If REDCapR isn't installed, use the previous version of the dataset.
+} else if( "0.9.8" < packageVersion("REDCapR") ) {
+  ds_2 <- REDCapR::redcap_read_oneshot(
+    redcap_uri = "https://bbmc.ouhsc.edu/redcap/api/",  # URL of REDCap Server.
+    token      = "F304DEC3793FECC3B6DEEFF66302CAD3",    # User-specific token/password.
+    guess_type = FALSE                                  # Keep all variables as strings/characters.
+  )$data  
+} else {
+  # Older versions of REDCapR don't have the `guess_type` parameter
+  ds_2 <- REDCapR::redcap_read_oneshot(
+    redcap_uri = "https://bbmc.ouhsc.edu/redcap/api/",  # URL of REDCap Server.
+    token      = "F304DEC3793FECC3B6DEEFF66302CAD3"     # User-specific token/password.
+  )$data %>% 
+    dplyr::mutate(
+      gender      = as.character(gender),
+      race        = as.character(race),
+      ethnicity   = as.character(ethnicity)
+    )
+}
 ```
 
 
@@ -195,8 +219,8 @@ table_nih_enrollment_pretty(
   d               = ds_3,
   d_lu_race       = ds_lu_race_3
 )
-
 ```
+
 Feedback Welcome
 =====================================================