Extend tests and Fixes for elixhausser quan 2005

NEWS.md

@@ -6,6 +6,10 @@
   * exclusions for less severer conditions when more severer conditions are flagged
   * Improved POA, NPOA, and EXEMPTPOA.  This came about from #20.
 
+* Make internal data.frame tool `mdcr_duplicated` data.table aware.
+
+* Elixhauser (Quan 2005) - added missing ICD-10 codes to the mappings
+
 ## New Features
 
 * `comorbidities()` will return a `tibble` with the input data is a `tbl_df`

R/utilities.R

@@ -132,7 +132,10 @@ mdcr_setnames <- function(x, old, new, ...) {
 mdcr_duplicated <- function(x, by = seq_along(x), ...) {
   stopifnot(is.data.frame(x))
   if (requireNamespace("data.table", quietly = TRUE) && inherits(x, "data.table")) {
-    rtn <- duplicated(x, by = by, ...)
+    # Flag this frame as data.table-aware so duplicated.data.table uses its
+    # optimized path instead of falling back to duplicated.data.frame.
+    .datatable.aware <- TRUE
+    rtn <- utils::getFromNamespace(x = 'duplicated.data.table', ns = "data.table")(x, by = by, ...)
   } else {
     rtn <- duplicated(x[, by, drop = FALSE], ...)
   }

data-raw/build_sysdata.R

@@ -52,6 +52,9 @@
 ..mdcr_internal_elixhauser_poa..          <- readRDS("./elixhauser/elixhauser_poa.rds")
 ..mdcr_internal_elixhauser_codes..        <- readRDS("./elixhauser/elixhauser_codes.rds")
 
+
+# All internl data sets need to have the ..mdcr_internal_ prefix and .. suffix.
+# This is expected in tests and in use within the package.
 usethis::use_data(
     ..mdcr_internal_pccc_codes..
   , ..mdcr_internal_pccc_conditions..

data-raw/elixhauser/regex_based_on_quan2005.txt

@@ -152,6 +152,11 @@ DEPRESS             | 9    | 1  | quan2005       | ^296\.[2,3,5]
 DEPRESS             | 9    | 1  | quan2005       | ^300\.4
 DEPRESS             | 9    | 1  | quan2005       | ^309
 DEPRESS             | 9    | 1  | quan2005       | ^311
+DEPRESS             | 10   | 1  | quan2005       | ^F20\.4
+DEPRESS             | 10   | 1  | quan2005       | ^F31\.[3-5]
+DEPRESS             | 10   | 1  | quan2005       | ^F3[2-3]
+DEPRESS             | 10   | 1  | quan2005       | ^F34\.1
+DEPRESS             | 10   | 1  | quan2005       | ^F4[1-3]\.2
 DM                  | 10   | 1  | quan2005       | ^E1[0-4]\.[0,1,9]
 DM                  | 9    | 1  | ahrq_web       | ^250\.[0-3]
 DM                  | 9    | 1  | ahrq_web       | ^648\.0
@@ -191,6 +196,7 @@ HTN_UNCX            | 9    | 1  | ahrq_web       | ^642\.0
 HTN_UNCX            | 9    | 1  | elixhauser1988 | ^401\.[1,9]
 HTN_UNCX            | 9    | 1  | quan2005       | ^401
 HYPOTHY             | 10   | 1  | quan2005       | ^E0[0-3]
+HYPOTHY             | 10   | 1  | quan2005       | ^E89\.0
 HYPOTHY             | 9    | 1  | ahrq_web       | ^243
 HYPOTHY             | 9    | 1  | ahrq_web       | ^244\.[0-2,8,9]
 HYPOTHY             | 9    | 1  | elixhauser1988 | ^243

tests/test-asserts.R

@@ -30,8 +30,6 @@ stopifnot(
   t01b = !("assert_scalar_logical" %in% getNamespaceExports("medicalcoder"))
 )
 
-# the method should only be used within methods and the error messages are
-# controlled:
 common_args <- list(data = mdcr, method = "pccc_v3.1", icd.codes = "code", poa = 1L)
 
 t02a <- tryCatchError(do.call(comorbidities, args = c(common_args, list(full.codes = TRUE))))