Merge branch 'master' into #51

ellessenne · Jul 12, 2022 · 7b36f16 · 7b36f16
2 parents 80674df + 5fb5bd0
commit 7b36f16
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Type: Package
 Package: comorbidity
-Version: 1.0.2
+Version: 1.0.3.9000
 Title: Computing Comorbidity Scores
 Description: Computing comorbidity indices and scores such as the weighted Charlson
   score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser
@@ -52,7 +52,7 @@ Suggests:
  rmarkdown,
  testthat
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Encoding: UTF-8
 LazyData: true
 ByteCompile: true

diff --git a/Makefile b/Makefile
@@ -7,7 +7,8 @@ pre_submission_test:
 	R -e "devtools::check_win_devel(quiet = TRUE)"
 	R -e "devtools::check_win_release(quiet = TRUE)"
 	R -e "devtools::check_win_oldrelease(quiet = TRUE)"
-	R -e "rhub::check_for_cran()"
+	R -e "devtools::check_mac_release(quiet = TRUE)"
+#	R -e "rhub::check_for_cran()"
 	R -e "rhub::check(platform = 'macos-m1-bigsur-release')"
 	make style
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,12 @@
+# comorbidity (development version)
+
+# comorbidity 1.0.3
+
+* Fixed a bug that did not allowed ID columns other than numeric (#55, thanks @norihikorihiko for reporting this).
+
 # comorbidity 1.0.2
 
-* The `copd` comorbidity for the Charlson index has been renamed to `cpd`, and the `ami` comorbidity for the Charlson index has been renamed to `mi` (#53, thanks @DrYan1102). Please be aware that this might break some old code if you were selecting comorbidities by name.
+* The `copd` and `ami` comorbidities for the Charlson index have been renamed to `cpd` and `mi`, respectively (#53, thanks @DrYan1102). Please be aware that this might break some old code if you were selecting comorbidities by name.
 
 * New dataset: ICD10-CM, 2022 version, named `icd10cm_2022`.
 

diff --git a/R/comorbidity.R b/R/comorbidity.R
@@ -112,22 +112,6 @@
 #' @export
 
 comorbidity <- function(x, id, code, map, assign0, labelled = TRUE, tidy.codes = TRUE) {
-  # set.seed(1)
-  # x <- data.frame(
-  #   id = 1,
-  #   code = sample_diag(10),
-  #   stringsAsFactors = FALSE
-  # )
-  # xa <- data.frame(id = 1:2, code = NA_character_)
-  # xm <- rbind(x, xa)
-  #
-  # x = xm
-  # id = "id"
-  # code = "code"
-  # map = "charlson_icd10_quan"
-  # assign0 = FALSE
-  # labelled = T
-  # tidy.codes = T
   ### Check arguments
   arg_checks <- checkmate::makeAssertCollection()
   # x must be a data.frame (or a data.table)

diff --git a/R/matchit.R b/R/matchit.R
@@ -28,8 +28,8 @@
   if (!is.null(x[["NA"]])) x[, `NA` := NULL]
 
   ### Restore IDs
-  x <- merge(x, backup, by = id, all.y = TRUE, )
-  data.table::setnafill(x = x, type = "const", fill = 0L)
+  x <- merge(x, backup, by = id, all.y = TRUE)
+  data.table::setnafill(x = x, type = "const", fill = 0L, cols = which(names(x) != id))
 
   ### Add missing columns
   for (col in names(regex)) {

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,8 +1,8 @@
 .onAttach <- function(libname, pkgname) {
-  tick <- stats::rbinom(n = 1, size = 1, prob = 0.4)
+  tick <- stats::rbinom(n = 1, size = 1, prob = 0.3)
   if (tick == 1) {
-    packageStartupMessage("This is {comorbidity} version 1.0.2.")
-    packageStartupMessage("A lot has changed since the last release on CRAN, please check-out breaking changes here:")
+    packageStartupMessage("This is {comorbidity} version 1.0.3.")
+    packageStartupMessage("A lot has changed since the pre-1.0.0 release on CRAN, please check-out breaking changes here:")
     packageStartupMessage("-> https://ellessenne.github.io/comorbidity/articles/C-changes.html")
   }
 }
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 # The {comorbidity} Package: Computing Comorbidity Scores <img src="man/figures/hex.png" width = "150" align="right" />
 
-Last updated: 2022-04-06
+Last updated: 2022-07-12
 
 <!-- badges: start -->
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,11 +1,10 @@
 ## Test environments
 
-* local R installation, R 4.1.2, Intel-based macOS Big Sur 11.6.2
+* local R installation, R 4.2.1, Intel-based macOS Monterey 12.4
 * ubuntu-latest (via GitHub Actions, devel, release, oldrel, 3.5, 3.4)
 * windows-latest (via GitHub Actions, devel, release, oldrel, 3.5, 3.4)
 * macos-latest (via GitHub Actions, release, oldrel)
 * windows (via winbuilder, devel, release, oldrel)
-* rhub (with rhub::check_for_cran())
 * arm64 mac (via macbuilder)
 * arm64 mac (via rhub::check(platform = 'macos-m1-bigsur-release'))
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html