fixes #177 and #142, many thanks to @overmar

jackwasey · May 1, 2020 · 9e51986 · 9e51986
2 parents d868b3f + 8e8e22c
commit 9e51986
Show file tree

Hide file tree

Showing 4 changed files with 21 additions and 13 deletions.
diff --git a/R/parse-comorbid.R b/R/parse-comorbid.R
@@ -44,11 +44,14 @@ icd9_fetch_ahrq_sas <- function() {
   )
 }
 
-icd10_fetch_ahrq_sas <- function(ver = "2016") {
+icd10_fetch_ahrq_sas <- function(ver = "2018") {
+  if (!ver %in% c("2016","2017","2018")) {
+    stop(ver," not currently available")
+  }
   .download_to_data_raw(
-    url = paste0(.ahrq_url_base, "comorbidityicd10/comformat_icd10cm_2016.txt"),
-    file_name = .get_versioned_raw_file_name("ahrq-comformat_icd10cm_2016.txt",
-      ver = "2016"
+    url = paste0(.ahrq_url_base, "comorbidityicd10/comformat_icd10cm_",ver,".txt"),
+    file_name = .get_versioned_raw_file_name(paste0("ahrq-comformat_icd10cm_",ver,".txt"),
+      ver = ver
     )
   )
 }
@@ -138,10 +141,10 @@ icd9_parse_ahrq_sas <- function(save_pkg_data = FALSE) {
 
 # This is in some ways simpler than that ICD-9 equivalent because I make no
 # attempt to find all the child codes.
-icd10_parse_ahrq_sas <- function(save_pkg_data = FALSE,
+icd10_parse_ahrq_sas <- function(version = "2018", save_pkg_data = FALSE,
                                  offline = TRUE) {
   assert_flag(save_pkg_data)
-  ahrq_info <- icd10_fetch_ahrq_sas()
+  ahrq_info <- icd10_fetch_ahrq_sas(ver = version)
   ahrq_sas_lines <- readLines(ahrq_info$file_path, warn = FALSE)
   icd10_map_ahrq <- sas_format_extract_rcomfmt(ahrq_sas_lines)
   unun <- function(x) unname(unlist(x))

diff --git a/R/update.R b/R/update.R
@@ -39,7 +39,7 @@
   icd9_generate_map_elix(save_pkg_data = TRUE)
   # ICD 10
   .parse_icd10cm_all(save_pkg_data = TRUE)
-  icd10_parse_ahrq_sas(save_pkg_data = TRUE)
+  icd10_parse_ahrq_sas(version = "2018", save_pkg_data = TRUE)
   .parse_icd10cm_cc(save_pkg_data = TRUE)
   icd10_generate_map_quan_elix(save_pkg_data = TRUE)
   icd10_generate_map_quan_deyo(save_pkg_data = TRUE)

diff --git a/data/icd10_map_ahrq.rda b/data/icd10_map_ahrq.rda
diff --git a/tests/testthat/test-build-maps-icd10.R b/tests/testthat/test-build-maps-icd10.R
@@ -32,12 +32,17 @@ test_that("icd-10 ahrq map is reproduced", {
   skip_on_appveyor()
   skip_on_travis()
   skip_on_cran()
-  skip_no_icd_data_raw(
-    icd10_fetch_ahrq_sas,
-    "AHRQ ICD-10 SAS must be downloaded with icd10_fetch_ahrq_sas"
-  )
-  expect_equivalent(
+  if (is.null(icd10_fetch_ahrq_sas())) {
+    skip("AHRQ ICD-10 SAS must be downloaded with icd10_fetch_ahrq_sas")
+  }
+  expect_identical(
     icd10_map_ahrq,
-    icd10_parse_ahrq_sas(save_pkg_data = FALSE)
+    icd10_parse_ahrq_sas(save_pkg_data = FALSE,version = "2018")
   )
+
+  expect_false(identical(
+    icd10_map_ahrq,
+    icd10_parse_ahrq_sas(save_pkg_data = FALSE,version = "2016")
+  ))
+
 })