remove unused code for lint checking in CI [ci skip]

export all S3 internal functions, as recommended.

Author: Jack O. Wasey

NAMESPACE

@@ -29,6 +29,8 @@ S3method(expand_minor,icd9)
 S3method(expand_range,character)
 S3method(expand_range,icd10cm)
 S3method(expand_range,icd9)
+S3method(expand_range_major,default)
+S3method(expand_range_major,icd10cm)
 S3method(expand_range_major,icd9)
 S3method(explain,default)
 S3method(explain,icd10)
@@ -52,13 +54,21 @@ S3method(get_invalid,comorbidity_map)
 S3method(get_invalid,default)
 S3method(get_invalid,icd10)
 S3method(get_invalid,icd9)
+S3method(get_major,icd10)
+S3method(get_major,icd9)
 S3method(get_valid,character)
 S3method(get_valid,icd10)
 S3method(get_valid,icd10cm)
 S3method(get_valid,icd9)
+S3method(get_visit_name,data.frame)
+S3method(get_visit_name,matrix)
 S3method(guess_version,character)
 S3method(guess_version,data.frame)
 S3method(guess_version,factor)
+S3method(guess_version,icd10)
+S3method(guess_version,icd10cm)
+S3method(guess_version,icd9)
+S3method(guess_version,icd9cm)
 S3method(is_billable,default)
 S3method(is_billable,icd10)
 S3method(is_billable,icd10cm)
@@ -68,6 +78,10 @@ S3method(is_defined,default)
 S3method(is_defined,icd10)
 S3method(is_defined,icd10cm)
 S3method(is_defined,icd9)
+S3method(is_major,default)
+S3method(is_major,icd10)
+S3method(is_major,icd10cm)
+S3method(is_major,icd9)
 S3method(is_valid,comorbidity_map)
 S3method(is_valid,default)
 S3method(is_valid,icd10)

R/RcppExports.R

@@ -237,6 +237,7 @@ icd9_decimal_to_short_cpp <- function(x) {
 #'   digits of numeric or V code, or first four digits of E code. This is the
 #'   part before the decimal, when a decimal point is used.
 #' @keywords internal manip
+#' @export
 get_major.icd9 <- function(x, short_code) {
     .Call(`_icd_icd9GetMajor`, x, short_code)
 }

R/comorbid.R

@@ -490,7 +490,7 @@ comorbid_quan_deyo <- function(x, ...)
                          icd10 = icd10_comorbid_quan_deyo), ...)
 
 #' @describeIn comorbid Calculate comorbidities using Charlson categories
-#'   according to Quan/Deyo ICD categories. Synonymouse with
+#'   according to Quan/Deyo ICD categories. Synonymous with
 #'   \code{link{comorbid_quan_deyo}} in this release.
 #' @export
 comorbid_charlson <- function(...)

R/guess.R

@@ -34,9 +34,20 @@
 guess_version <- function(x, short_code, ...)
   UseMethod("guess_version")
 
+#' @keywords internal
+#' @export
 guess_version.icd9 <- function(x, short_code, ...) "icd9" #nocov
+
+#' @keywords internal
+#' @export
 guess_version.icd9cm <- function(x, short_code, ...) "icd9cm" #nocov
+
+#' @keywords internal
+#' @export
 guess_version.icd10 <- function(x, short_code, ...) "icd10" #nocov
+
+#' @keywords internal
+#' @export
 guess_version.icd10cm <- function(x, short_code, ...) "icd10cm" #nocov
 
 #' @describeIn guess_version Guess version of ICD codes in a factor

R/ranges.R

@@ -140,6 +140,7 @@ expand_range_major <- function(start, end) {
 #' @describeIn expand_range_major Expand range of top-level, 'major' codes
 #'   of unknown type
 #' @keywords internal
+#' @export
 expand_range_major.default <- function(start, end) {
   icd_ver <- guess_pair_version(start, end, short_code = TRUE)
   if (icd_ver == "icd9")
@@ -150,6 +151,7 @@ expand_range_major.default <- function(start, end) {
 
 #' @describeIn expand_range_major Expand range of top-level ICD-10 codes
 #' @keywords internal
+#' @export
 expand_range_major.icd10cm <- function(start, end) {
 
   # codes may have alphabetic characters in 3rd position, so can't just do

R/util.R

@@ -201,6 +201,8 @@ get_visit_name <- function(x, visit_name = NULL) {
 .visit_name_guesses <- c("visit.?Id", "patcom", "encounter.?id", "enc.?id",
                          "in.*enc", "out.*enc", "encounter", "visit", "enc")
 
+#' @keywords internal
+#' @export
 get_visit_name.data.frame <- function(x, visit_name = NULL) {
   assert_data_frame(x, min.cols = 1, col.names = "named")
 
@@ -221,6 +223,8 @@ get_visit_name.data.frame <- function(x, visit_name = NULL) {
   visit_name
 }
 
+#' @keywords internal
+#' @export
 get_visit_name.matrix <- function(x, visit_name = NULL) {
   stop("matrices of comorbidity data are expected to be of logical type, and have row names corresponding to the visit or patient.")
 }

R/valid.R

@@ -479,6 +479,7 @@ get_major <- function(x) {
 #'   can re-use C++ ICD-9 version: just grabbing the first three characters,
 #'   after all, and this is much easier in ICD-10 then ICD-9
 #' @keywords internal
+#' @export
 get_major.icd10 <- function(x) {
   substr(trim(x), 1L, 3L)
 }
@@ -492,6 +493,7 @@ is_major <- function(x) {
 
 #' @describeIn is_major Default method which guesses version
 #' @keywords internal
+#' @export
 is_major.default <- function(x) {
   switch(
     guess_version(x),
@@ -505,6 +507,7 @@ is_major.default <- function(x) {
 
 #' @describeIn is_major check whether a code is an ICD-10 major
 #' @keywords internal
+#' @export
 is_major.icd10 <- function(x) {
   assert_character(x)
   # if not know whether ICD-10-CM, then use broader definition
@@ -515,13 +518,15 @@ is_major.icd10 <- function(x) {
 #'   Currently uses \code{stringr} which uses \code{stringi} which should be
 #'   quite fast, but does suffer from handling Unicode, locales, etc.
 #' @keywords internal
+#' @export
 is_major.icd10cm <- function(x) {
   assert_character(x)
   grepl(re_just_ws(re_icd10cm_major), trim(x), perl = TRUE)
 }
 
 #' @describeIn is_major check whether a code is an ICD-9 major
 #' @keywords internal
+#' @export
 is_major.icd9 <- function(x) {
   x <- trim(x)
   nchar(x) - icd9_is_e(x) < 4

R/zzz.R

@@ -52,7 +52,6 @@ release_questions <- function() {
     "Does every file have correct licence information?",
     "Is spelling correct everywhere? E.g. aspell_package_Rd_files('.')",
     # code quality:
-    "Has the development branch been merged/rebased into master?",
     "Are you happy with the code coverage?",
     "Is every SEXP PROTECT()ed and UNPROTECT()ed, when appropriate?",
     "Are all public S3 classes all exported? use devtools::missing_s3()",
@@ -76,7 +75,6 @@ release_questions <- function() {
     "Have all unnecessary files been ignored in built archive? Especially
       thinking of autoconfigure stuff. Look in the final built archive
       before submitting to CRAN?",
-    "Has .*_alt\\.[Rr]$ been reactivated in .Rbuildignore?",
     # not CRAN
     "Are github pages site refreshed from latest documentation?",
     NULL

appveyor.yml

@@ -23,7 +23,6 @@ before_build:
   - ls -aR
   - rm .Rinstignore  # do install everything for testing
   - sed -i'' -e '/.*[Dd]ata.*/d' .Rbuildignore # do include data for testing, some data not in github though
-  - sed -i'' -e '/\.lintr/d' .Rbuildignore
   - Rscript -e "install.packages('Rcpp', repos = 'https://cloud.r-project.org/'); Rcpp::compileAttributes()" # make sure Rcpp generated code is made, if not checked in to repo
 
 build_script:

man/comorbid.Rd

@@ -272,6 +272,7 @@ CV icd9DecimalToShort(
 //'   digits of numeric or V code, or first four digits of E code. This is the
 //'   part before the decimal, when a decimal point is used.
 //' @keywords internal manip
+//' @export
 //[[Rcpp::export(name="get_major.icd9")]]
 CV icd9GetMajor(const CV x, const bool short_code) {
   if (short_code) {