Release 0.1.3 to CRAN (#170)

Closes #142
NeuroShepherd · Jan 29, 2025 · 4da1769 · 4da1769
2 parents aa8c969 + 1204829
commit 4da1769
Show file tree

Hide file tree

Showing 12 changed files with 33 additions and 13 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -22,3 +22,4 @@ $run_dev.*
 ^.lintr$
 ^cran-comments\.md$
 ^CITATION\.cff$
+^CRAN-SUBMISSION$
diff --git a/CITATION.cff b/CITATION.cff
@@ -8,11 +8,11 @@ message: 'To cite package "ordinalsimr" in publications use:'
 type: software
 license: MIT
 title: 'ordinalsimr: Compare Ordinal Endpoints Using Simulations'
-version: 0.1.1
+version: 0.1.3
 doi: 10.5281/zenodo.14697216
 abstract: Simultaneously evaluate multiple ordinal outcome measures. Applied data
   analysts in particular are faced with uncertainty in choosing appropriate statistical
-  tests for ordinal data. The included Shiny applications allows users to simulate
+  tests for ordinal data. The included 'shiny' application allows users to simulate
   outcomes given different ordinal data distributions.
 authors:
 - family-names: Callahan
@@ -35,7 +35,7 @@ preferred-citation:
   copyright: MIT
   abstract: Simultaneously evaluate multiple ordinal outcome measures. Applied data
     analysts in particular are faced with uncertainty in choosing appropriate statistical
-    tests for ordinal data. The included Shiny applications allows users to simulate
+    tests for ordinal data. The included 'shiny' applications allows users to simulate
     outcomes given different ordinal data distributions.
 repository-code: https://github.com/NeuroShepherd/ordinalsimr
 url: https://neuroshepherd.github.io/ordinalsimr/

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: ordinalsimr
 Title: Compare Ordinal Endpoints Using Simulations
-Version: 0.1.1
+Version: 0.1.3
 Authors@R: 
     person(given = "Pat",
            family = "Callahan",
            role = c("aut", "cre", "cph"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-1769-7580"))
-Description: Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included Shiny applications allows users to simulate outcomes given different ordinal data distributions.
+Description: Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included 'shiny' application allows users to simulate outcomes given different ordinal data distributions.
 License: MIT + file LICENSE
 Imports: 
     assertthat,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# ordinalsimr 0.1.3
+
+* Updates to match CRAN submission standards
+
 # ordinalsimr 0.1.1
 
 * Create DOI via Zenodo and add to CITATION file

diff --git a/R/run_app.R b/R/run_app.R
@@ -4,6 +4,8 @@
 #' See `?golem::get_golem_options` for more details.
 #' @inheritParams shiny::shinyApp
 #'
+#' @return NULL, the function is called for its side effects
+#'
 #' @export
 #' @importFrom shiny shinyApp
 #' @importFrom golem with_golem_options

diff --git a/R/run_simulations.R b/R/run_simulations.R
@@ -22,7 +22,7 @@
 #'   sample_prob = c(0.5, 0.5),
 #'   prob0 = c(0.1, 0.2, 0.3, 0.4),
 #'   prob1 = c(0.6, 0.2, 0.1, 0.1),
-#'   niter = 50
+#'   niter = 40
 #' )
 #'
 run_simulations <- function(sample_size, sample_prob, prob0, prob1, niter, included = "all",

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,11 @@
-## R CMD check results
+## Resubmission -- 0.1.3
 
-0 errors | 0 warnings | 1 note
+This is a resubmission. In this version I have:
+
+* Reformatted the DESCRIPTION file to follow the CRAN guidelines for writing package names.
+* Updated code in the `ordinalsimr-options` vignette to reset the options to their default values after the vignette is run.
+* Reduced the number of simulation iterations from 50 to 40 in the example for `run_simulations.R` to keep the run time for examples under 5s. Previously, the example took 5.019s to run on r-devel-linux-x86_64-debian-gcc.
+* A @return tag was added to the `run_app` function in the `run_app.R` file, and indicates the function is called for its side-effects
+
+Additionally, we are currently working on a manuscript that will be added to the DESCRIPTION and CITATION files in a later release.
 
-* This is a new release.
-* This package imports the {rms} package which depends on R (>= 4.4.0).
diff --git a/inst/CITATION b/inst/CITATION
@@ -19,7 +19,7 @@ bibentry(
   urldate = "2025-01-19",
   copyright = "MIT",
   date = "2025-01",
-  abstract = "Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included Shiny applications allows users to simulate outcomes given different ordinal data distributions."
+  abstract = "Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included 'shiny' applications allows users to simulate outcomes given different ordinal data distributions."
 )
 
 
diff --git a/man/ordinalsimr-package.Rd b/man/ordinalsimr-package.Rd
diff --git a/man/run_app.Rd b/man/run_app.Rd
diff --git a/man/run_simulations.Rd b/man/run_simulations.Rd
diff --git a/vignettes/ordinalsimr-options.Rmd b/vignettes/ordinalsimr-options.Rmd
@@ -12,6 +12,8 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
+
+start_options <- options()
 ```
 
 ```{r setup}
@@ -101,6 +103,9 @@ get_ordinalsimr_options()
 
 
 
+```{r, include = FALSE}
+options(start_options)
+```