use roxygen2 5.00 (updates all documentation), minor doc fixes in exp…

…lain.R, use "_PACKAGE" in package docs, set CXXFLAGS in configure.ac
jackwasey · Nov 2, 2015 · 1757ede · 1757ede
1 parent eed4ff8
commit 1757ede
Show file tree

Hide file tree

Showing 85 changed files with 152 additions and 273 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -37,11 +37,13 @@ Suggests:
     ggplot2,
     digest,
     xtable,
-    rmarkdown
+    rmarkdown,
+    roxygen2 (>= 5.0.0)
 LazyData: true
 LazyDataCompression: xz
 BugReports: https://github.com/jackwasey/icd9/issues
 License: GPL-3
 Copyright: See file (inst/)COPYRIGHTS
 VignetteBuilder: knitr
 LinkingTo: Rcpp
+RoxygenNote: 5.0.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(icd9Charlson,data.frame)
 S3method(icd9Explain,character)

diff --git a/R/explain.R b/R/explain.R
@@ -152,9 +152,9 @@ icd9GuessIsShort <- function(icd9) {
 #'   respective chapters, sub-chapters, etc.. The querying of the web page to
 #'   get these is already done, and the results saved in the lists
 #'   \code{icd9Chapters} etc which define ranges.
-#' @param icd9-any
-#' @param isShort
-#' @param invalid
+#' @template icd9-any
+#' @template isShort
+#' @template verbose
 #' @keywords internal
 icd9GetChapters <- function(icd9, isShort = icd9GuessIsShort(icd9), verbose = FALSE) {
   # set up comorbidity maps for chapters/sub/major group, then loop through each

diff --git a/R/icd9-package.R b/R/icd9-package.R
@@ -15,15 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with icd9. If not, see <http:#www.gnu.org/licenses/>.
 
-#' @title tools for working with ICD-9 codes, and finding comorbidities
-#' @description Calculate comorbidities, and perform fast and accurate
-#'   validation, conversion, manipulation, filtering and comparison of ICD-9-CM
-#'   (clinical modification) codes. ICD-9 codes appear numeric but leading and
-#'   trailing zeroes, and both decimal and non-decimal "short" format codes
-#'   exist. The package enables a work flow from raw lists of ICD-9 codes from
-#'   hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
-#'   from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
-#'
+#' @details
 #'   \describe{
 #'
 #'   \item{Comorbidities}{ \code{\link{icd9Comorbid}} determines co-morbidities
@@ -79,6 +71,8 @@
 #'   contains definitions of chapters, sub-chapters and three-digit groups.}
 #'
 #'   }
+#'
+"_PACKAGE"
 #' @docType package
 #' @name icd9-package
 #' @aliases icd9 package-icd9

diff --git a/configure b/configure
@@ -2272,6 +2272,10 @@ CPP=`"${R_BIN}" CMD config CPP`
 CFLAGS=`"${R_BIN}" CMD config CFLAGS`
 CPPFLAGS=`"${R_BIN}" CMD config CPPFLAGS`
 CXXFLAGS=`"${R_BIN}" CMD config CXXFLAGS`
+# Writing R Extensions recommends the following, but I don't seem to need it, perhaps because I disable C++11 in some systems when it won't work with OpenMP:
+# CXX1X=`"${R_BIN}" CMD config CXX1X`
+# CXX1XSTD=`"${R_BIN}" CMD config CXX1XSTD`
+CXXFLAGS=`"${R_BIN}" CMD config CXXFLAGS`
 LIBS="${PKG_LIBS}"
 
 ac_ext=c

diff --git a/configure.ac b/configure.ac
@@ -36,6 +36,10 @@ CPP=`"${R_BIN}" CMD config CPP`
 CFLAGS=`"${R_BIN}" CMD config CFLAGS`
 CPPFLAGS=`"${R_BIN}" CMD config CPPFLAGS`
 CXXFLAGS=`"${R_BIN}" CMD config CXXFLAGS`
+# Writing R Extensions recommends the following, but I don't seem to need it, perhaps because I disable C++11 in some systems when it won't work with OpenMP:
+# CXX1X=`"${R_BIN}" CMD config CXX1X`
+# CXX1XSTD=`"${R_BIN}" CMD config CXX1XSTD`
+CXXFLAGS=`"${R_BIN}" CMD config CXXFLAGS`
 LIBS="${PKG_LIBS}"
 
 AC_CHECK_HEADER([string.h])

diff --git a/man/ahrqComorbid.Rd b/man/ahrqComorbid.Rd
diff --git a/man/ahrqComorbidAll.Rd b/man/ahrqComorbidAll.Rd
diff --git a/man/convert.Rd b/man/convert.Rd
diff --git a/man/cr.Rd b/man/cr.Rd
diff --git a/man/elixComorbid.Rd b/man/elixComorbid.Rd
diff --git a/man/elixComorbidNames.Rd b/man/elixComorbidNames.Rd
diff --git a/man/expandRangeWorker.Rd b/man/expandRangeWorker.Rd
diff --git a/man/factor_.Rd b/man/factor_.Rd
diff --git a/man/fastIntToString.Rd b/man/fastIntToString.Rd
diff --git a/man/generateSysData.Rd b/man/generateSysData.Rd
diff --git a/man/icd9-package.Rd b/man/icd9-package.Rd
diff --git a/man/icd9AddLeadingZeroes.Rd b/man/icd9AddLeadingZeroes.Rd
diff --git a/man/icd9Benchmark.Rd b/man/icd9Benchmark.Rd
diff --git a/man/icd9Billable.Rd b/man/icd9Billable.Rd
diff --git a/man/icd9Chapters.Rd b/man/icd9Chapters.Rd
diff --git a/man/icd9ChaptersToMap.Rd b/man/icd9ChaptersToMap.Rd
diff --git a/man/icd9Charlson.Rd b/man/icd9Charlson.Rd
diff --git a/man/icd9Children.Rd b/man/icd9Children.Rd
diff --git a/man/icd9Comorbid.Rd b/man/icd9Comorbid.Rd
diff --git a/man/icd9ComorbidDfToMat.Rd b/man/icd9ComorbidDfToMat.Rd
diff --git a/man/icd9ComorbidMatToDf.Rd b/man/icd9ComorbidMatToDf.Rd
diff --git a/man/icd9Condense.Rd b/man/icd9Condense.Rd