Ahrq 2026

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: medicalcoder
 Title: A Package for Working with ICD Codes and Comorbidity Algorithms
-Version: 0.7.0.9000
+Version: 0.7.0.9001
 Authors@R: c(
     person(given = "Peter",   family = "DeWitt",    email = "[email protected]",      role = c("aut", "cre", "cov"), comment = c(ORCID = "0000-0002-6391-0795")),
     person(given = "Tell",    family = "Bennett",   email = "[email protected]",      role = c("ctb"),               comment = c(ORCID = "0000-0003-1483-4236")),

NEWS.md

@@ -7,12 +7,18 @@
   change will generally result in less computation time than base R
   `data.frames` (`data.tables` require even less time).
 
+* Add the `elixhauser_ahrq2026` method for `comorbidities()` (#32)
+
 ## Bug Fixes
 
 * `summary.medicalcoder_comorbidites()` no longer crashes when a zero row input
-  is passed in. Consisently return `NA` instead of `NaN` when counts are zeros.
+  is passed in. Consistently return `NA` instead of `NaN` when counts are zeros.
   (#26, #27)
 
+* Improve the conditional and multiple comorbidities mapped by a code under AHRQ
+  ICD-10 codes for fiscal years 2023 through 2026.  The bug was found and fixed
+  as part of the extension #32.
+
 ## Other Changes
 
 * Extend and improve the internal ICD-9 database to distinguish between CDC and
@@ -25,13 +31,13 @@
   `mdcr_set()`, and added inline guidance in the longitudinal section of
   `comorbidities()` to explain the first-occurrence logic.
 
-* Improve cumulative flagging to apply first-occurrence logic more effecently.
+* Improve cumulative flagging to apply first-occurrence logic more efficiently.
 
 * Extend documentation for the expected default behavior between the
   present-on-admission flags and `flag.method` argument in `comorbidities()`
   (re: #28)
 
-* Add `mdcr_unique()` to the data.frame utilties. This reduced the computational
+* Add `mdcr_unique()` to the data.frame utilities. This reduced the computational
   time required to apply `comorbidities()` to `tibble`s and `data.table`s. (#31)
 
 # medicalcoder 0.7.0
@@ -42,7 +48,7 @@
   * 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.
+* Make internal data.frame tool `mdcr_duplicated()` data.table aware.
 
 * Elixhauser (Quan 2005) - added missing ICD-10 codes to the mappings
 

R/comorbidities.R

@@ -141,8 +141,8 @@
 #' * Elixhauser Comorbidities:
 #'
 #'   * Agency for Healthcare Research and Quality (AHRQ). Elixhauser
-#'     Comorbidity Software Refined for ICD-10-CM Diagnoses, v2025.1 \[Internet\].
-#'     2025. Available from:
+#'     Comorbidity Software Refined for ICD-10-CM Diagnoses, v2026.1 \[Internet\].
+#'     2026. Available from:
 #'     https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp
 #'
 #' @seealso
@@ -676,7 +676,7 @@ comorbidities_methods <- function() {
       "charlson_cdmf2019",
       "elixhauser_elixhauser1988", "elixhauser_ahrq_web", "elixhauser_quan2005",
       "elixhauser_ahrq2022", "elixhauser_ahrq2023", "elixhauser_ahrq2024",
-      "elixhauser_ahrq2025", "elixhauser_ahrq_icd10")
+      "elixhauser_ahrq2025", "elixhauser_ahrq2026", "elixhauser_ahrq_icd10")
 }
 
 
@@ -689,7 +689,7 @@ comorbidities_methods <- function() {
     "transplant_flag", "tech_dep_flag",
     "pccc_v3.1", "pccc_v3.0", "pccc_v2.1", "pccc_v2.0",
     "elixhauser_ahrq_web", "elixhauser_elixhauser1988", "elixhauser_quan2005",
-    "elixhauser_ahrq2022", "elixhauser_ahrq2023", "elixhauser_ahrq2024", "elixhauser_ahrq2025",
+    "elixhauser_ahrq2022", "elixhauser_ahrq2023", "elixhauser_ahrq2024", "elixhauser_ahrq2025", "elixhauser_ahrq2026",
     "elixhauser_ahrq_icd10",
     "charlson_cdmf2019", "charlson_deyo1992", "charlson_quan2005", "charlson_quan2011"
   )

R/elixhauser.R

@@ -43,7 +43,6 @@
   rtn <- mdcr_set(rtn, j = "readmission_index", value = results$readmission_index)
   rownames(rtn) <- NULL
   rtn
-
 }
 
 .elixhauser_post2022 <- function(ccc, id.vars, iddf, cmrb, poa.var, primarydx.var, method) {
@@ -93,23 +92,37 @@
     XANYPOA[cbind(ri[keep], ci[keep])] <- 1L
   }
 
-  # Assign comorbidities which are nutral to POA
+  # Assign comorbidities which are neutral to POA
   from_to <-
     c("DRUG_ABUSEPSYCHOSES" = "DRUG_ABUSE",
       "HFHTN_CX" = "HTN_CX",
       "HTN_CXRENLFL_SEV"= "HTN_CX",
       "HFHTN_CXRENLFL_SEV"= "HTN_CX",
       "ALCOHOLLIVER_MLD" = "ALCOHOL",
-      "VALVE_AUTOIMMUNE" = "AUTOIMMUNE"
+      "VALVE_AUTOIMMUNE" = "AUTOIMMUNE",
+      "LIVER_MLD_NEURO" = "LIVER_MLD",
+      "LIVER_MLD_NEURO" = "NEURO_OTH",
+      "NEURO_OTH_SEIZ" = "NEURO_OTH",
+      "NEURO_OTH_SEIZ" = "NEURO_SEIZ",
+      "LIVER_MLD_PULMCIRC" = "LIVER_MLD",
+      "LIVER_MLD_PULMCIRC" = "PULMCIRC"
     )
 
   for (i in seq_len(length(from_to))) {
     f <- names(from_to)[i]
     t <- unname(from_to[i])
-          XPOA[      XPOA[, f] == 1L, t] <- 1L
-    XPOAEXEMPT[XPOAEXEMPT[, f] == 1L, t] <- 1L
-       XANYPOA[   XANYPOA[, f] == 1L, t] <- 1L
-         XNPOA[     XNPOA[, f] == 1L, t] <- 1L
+    if (f %in% colnames(XPOA)) {
+      XPOA[XPOA[, f] == 1L, t] <- 1L
+    }
+    if (f %in% colnames(XPOAEXEMPT)) {
+      XPOAEXEMPT[XPOAEXEMPT[, f] == 1L, t] <- 1L
+    }
+    if (f %in% colnames(XANYPOA)) {
+      XANYPOA[XANYPOA[, f] == 1L, t] <- 1L
+    }
+    if (f %in% colnames(XNPOA)) {
+      XNPOA[XNPOA[, f] == 1L, t] <- 1L
+    }
   }
 
   # flag if poa expempt or POA
@@ -128,8 +141,12 @@
   for (i in seq_len(length(from_to))) {
     f <- names(from_to)[i]
     t <- unname(from_to[i])
-          XPOA[      XPOA[, f] == 1L, t] <- 1L
-    XPOAEXEMPT[XPOAEXEMPT[, f] == 1L, t] <- 1L
+    if (f %in% colnames(XPOA)) {
+      XPOA[XPOA[, f] == 1L, t] <- 1L
+    }
+    if (f %in% colnames(XPOAEXEMPT)) {
+      XPOAEXEMPT[XPOAEXEMPT[, f] == 1L, t] <- 1L
+    }
   }
 
   # CBVD_NPOA is unique in that it requires that the condition is not POA

README.Rmd

@@ -274,14 +274,15 @@ vignette(topic = "charlson", package = "medicalcoder")
   * `method = elixhauser_elixhauser1988`
 * [Quan et al. (2005)](https://doi.org/10.1097/01.mlr.0000182534.19832.83)
   * `method = elixhauser_quan2005`
-* AHRQ (2017, 2022, 2023, 2024, 2025, ICD10)
+* AHRQ (2017, 2022, 2023, 2024, 2025, 2026, ICD10)
   * [For ICD-9 codes](https://hcup-us.ahrq.gov/toolssoftware/comorbidity/comorbidity.jsp)
     * `method = elixhauser_ahrq_web`
   * [For ICD-10 codes](https://hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp)
     * `method = elixhauser_ahrq2022`
     * `method = elixhauser_ahrq2023`
     * `method = elixhauser_ahrq2024`
     * `method = elixhauser_ahrq2025`
+    * `method = elixhauser_ahrq2026`
     * `method = elixhauser_ahrq_icd10`
 
 ```{r}

README.md

@@ -312,14 +312,15 @@ vignette(topic = "charlson", package = "medicalcoder")
   * `method = elixhauser_elixhauser1988`
 * [Quan et al. (2005)](https://doi.org/10.1097/01.mlr.0000182534.19832.83)
   * `method = elixhauser_quan2005`
-* AHRQ (2017, 2022, 2023, 2024, 2025, ICD10)
+* AHRQ (2017, 2022, 2023, 2024, 2025, 2026, ICD10)
   * [For ICD-9 codes](https://hcup-us.ahrq.gov/toolssoftware/comorbidity/comorbidity.jsp)
     * `method = elixhauser_ahrq_web`
   * [For ICD-10 codes](https://hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp)
     * `method = elixhauser_ahrq2022`
     * `method = elixhauser_ahrq2023`
     * `method = elixhauser_ahrq2024`
     * `method = elixhauser_ahrq2025`
+    * `method = elixhauser_ahrq2026`
     * `method = elixhauser_ahrq_icd10`
 
 

data-raw/elixhauser/elixhauser.R

@@ -41,10 +41,7 @@ codes <- codes[,
   "ahrq_web",
   "elixhauser1988",
   "quan2005",
-  "ahrq2022",
-  "ahrq2023",
-  "ahrq2024",
-  "ahrq2025",
+  sort(grep("ahrq\\d{4}", names(codes), value = TRUE)),
   "ahrq_icd10")]
 
 # Which conditions require a POA required flag?

data-raw/elixhauser/elixhauser_ahrq_icd10.R

@@ -9,6 +9,7 @@
 #   ahrq/CMR_v2023-1.zip
 #   ahrq/CMR_v2024-1.zip
 #   ahrq/CMR_v2025.1.zip
+#   ahrq/CMR-v2026-1.zip
 #   ../icd/icd_codes.rds
 #
 # output:
@@ -47,38 +48,43 @@ if (interactive()) {
   unzip("ahrq/CMR_v2023-1.zip", list = TRUE)  # AHRQ based on ICD-10
   unzip("ahrq/CMR_v2024-1.zip", list = TRUE)  # AHRQ based on ICD-10
   unzip("ahrq/CMR_v2025.1.zip", list = TRUE)  # AHRQ based on ICD-10
+  unzip("ahrq/CMR-v2026-1.zip", list = TRUE)  # AHRQ based on ICD-10
 }
 
 unzip("ahrq/CMR_v2022-1.zip", exdir = tmpdir)
 unzip("ahrq/CMR_v2023-1.zip", exdir = tmpdir)
 unzip("ahrq/CMR_v2024-1.zip", exdir = tmpdir)
 unzip("ahrq/CMR_v2025.1.zip", exdir = tmpdir, junkpaths = TRUE)
+unzip("ahrq/CMR-v2026-1.zip", exdir = tmpdir)
 
 ################################################################################
 # import all the SAS Programs for the ICD-10 version of Elixhauser
 
 format_programs <-
   list(
-    "ahrq2022" = scan(file = paste0(tmpdir, "/CMR_Format_Program_v2022-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2023" = scan(file = paste0(tmpdir, "/CMR_Format_Program_v2023-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2024" = scan(file = paste0(tmpdir, "/CMR_Format_Program_v2024-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2025" = scan(file = paste0(tmpdir, "/CMR_Format_Program_v2025-1.sas"), what = character(), sep = "\n", quiet = !interactive())
+    "ahrq2022" = scan(file = file.path(tmpdir, "CMR_Format_Program_v2022-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2023" = scan(file = file.path(tmpdir, "CMR_Format_Program_v2023-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2024" = scan(file = file.path(tmpdir, "CMR_Format_Program_v2024-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2025" = scan(file = file.path(tmpdir, "CMR_Format_Program_v2025-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2026" = scan(file = file.path(tmpdir, "CMR_Format_Program_v2026-1.sas"), what = character(), sep = "\n", quiet = !interactive())
   )
 
 mapping_programs <-
   list(
-    "ahrq2022" = scan(file = paste0(tmpdir, "/CMR_Mapping_Program_v2022-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2023" = scan(file = paste0(tmpdir, "/CMR_Mapping_Program_v2023-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2024" = scan(file = paste0(tmpdir, "/CMR_Mapping_Program_v2024-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2025" = scan(file = paste0(tmpdir, "/CMR_Mapping_Program_v2025-1.sas"), what = character(), sep = "\n", quiet = !interactive())
+    "ahrq2022" = scan(file = file.path(tmpdir, "CMR_Mapping_Program_v2022-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2023" = scan(file = file.path(tmpdir, "CMR_Mapping_Program_v2023-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2024" = scan(file = file.path(tmpdir, "CMR_Mapping_Program_v2024-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2025" = scan(file = file.path(tmpdir, "CMR_Mapping_Program_v2025-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2026" = scan(file = file.path(tmpdir, "CMR_Mapping_Program_v2026-1.sas"), what = character(), sep = "\n", quiet = !interactive())
   )
 
 index_programs <-
   list(
-    "ahrq2022" = scan(file = paste0(tmpdir, "/CMR_Index_Program_v2022-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2023" = scan(file = paste0(tmpdir, "/CMR_Index_Program_v2023-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2024" = scan(file = paste0(tmpdir, "/CMR_Index_Program_v2024-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
-    "ahrq2025" = scan(file = paste0(tmpdir, "/CMR_Index_Program_v2025-1.sas"), what = character(), sep = "\n", quiet = !interactive())
+    "ahrq2022" = scan(file = file.path(tmpdir, "CMR_Index_Program_v2022-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2023" = scan(file = file.path(tmpdir, "CMR_Index_Program_v2023-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2024" = scan(file = file.path(tmpdir, "CMR_Index_Program_v2024-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2025" = scan(file = file.path(tmpdir, "CMR_Index_Program_v2025-1.sas"), what = character(), sep = "\n", quiet = !interactive()),
+    "ahrq2026" = scan(file = file.path(tmpdir, "CMR_Index_Program_v2026-1.sas"), what = character(), sep = "\n", quiet = !interactive())
   )
 
 ################################################################################
@@ -100,29 +106,31 @@ values <-
   lapply(format_programs, get_value_start_stop) |>
   rbindlist(idcol = "version")
 
-build_comfmt <-
-  function(x) {
-    x <- sub(pattern = '=', replacement = "->", x)
-    x <- sub(pattern = '-> \\"(.+)\\"', replacement = ") -> \\1;", x = x)
-    strt <- grep("->", x) + 1
-    x[1] <- paste("c(", x[1])
-    x[strt] <- paste("c(", x[strt])
-    other_idx <- grep("other", x)
-    x <- x[-seq(other_idx, length(x))]
-    tmpfile <- tempfile()
-    cat(x, file = tmpfile)
-    e <- new.env()
-    source(tmpfile, local = e)
-    as.list(e)
-  }
+build_comfmt <- function(x) {
+  x <- sub(pattern = '=', replacement = "->", x)
+  x <- sub(pattern = '-> \\"(.+)\\"', replacement = ") -> \\1;", x = x)
+  strt <- grep("->", x) + 1
+  x[1] <- paste("c(", x[1])
+  x[strt] <- paste("c(", x[strt])
+  other_idx <- grep("other", x)
+  x <- x[-seq(other_idx, length(x))]
+  tmpfile <- tempfile()
+  cat(x, file = tmpfile)
+  e <- new.env()
+  source(tmpfile, local = e)
+  as.list(e)
+}
 
 build_poaexmpt <- function(x) {
   other_idx <- grep("other", x)
   x <- x[-seq(other_idx, length(x))]
+  # for 2022 - 2025 the last element ended with "1"
+  # for 2026 the last element ended with '1'
+  # Change from double quotes to single quotes.
   x <- sub('= \\"1\\"', ')', x)
+  x <- sub("= '1'", ')', x)
   x <- trimws(x)
   x[1] <- paste("poaexmpt <- c(", x[1])
-  x
   tmpfile <- tempfile()
   cat(x, file = tmpfile)
   e <- new.env()
@@ -253,7 +261,9 @@ elixhauser_poa <-
   list("ahrq2022" = readxl::read_xlsx(paste0(tmpdir, "/CMR-Reference-File-v2022-1.xlsx"), sheet = 2, skip = 1),
        "ahrq2023" = readxl::read_xlsx(paste0(tmpdir, "/CMR-Reference-File-v2023-1.xlsx"), sheet = 2, skip = 1),
        "ahrq2024" = readxl::read_xlsx(paste0(tmpdir, "/CMR-Reference-File-v2024-1.xlsx"), sheet = 2, skip = 1),
-       "ahrq2025" = readxl::read_xlsx(paste0(tmpdir, "/CMR-Reference-File-v2025-1.xlsx"), sheet = 2, skip = 1))
+       "ahrq2025" = readxl::read_xlsx(paste0(tmpdir, "/CMR-Reference-File-v2025-1.xlsx"), sheet = 2, skip = 1),
+       "ahrq2026" = readxl::read_xlsx(paste0(tmpdir, "/CMR-Reference-File-v2026-1.xlsx"), sheet = 2, skip = 1)
+  )
 
 elixhauser_poa <- lapply(elixhauser_poa, setDT)
 
@@ -279,15 +289,26 @@ elixhauser_poa[, condition := sub("CMR_", "", condition)]
 
 # Extend conditions -- several of the conditions in the elixhauser_poa set are
 # catch alls and more granular conditions are in the codes.  Extend the
-# elixhauser_poa set to include th more granular conditions
+# elixhauser_poa set to include the more granular conditions
 #
-#> qwraps2::set_diff(elixhauser_poa$condition, elixhauser_codes$condition)
+# 2026 added a new condition, LIVER_MLD_PULMCIRC
+#> qwraps2::set_diff(
+#>   elixhauser_codes[ahrq2025 == 1, condition],
+#>   elixhauser_codes[ahrq2026 == 1, condition]
+#> )
 #+ Total number of unique values: 49
+#+ Number of elements in both elixhauser_codes[ahrq2025 == 1, condition] and elixhauser_codes[ahrq2026 == 1, condition]: 48
+#+ Number of elements only in elixhauser_codes[ahrq2025 == 1, condition]: 0
+#+ Number of elements only in elixhauser_codes[ahrq2026 == 1, condition]: 1
+#+   unique elements: LIVER_MLD_PULMCIRC
+
+#> qwraps2::set_diff(elixhauser_poa$condition, elixhauser_codes$condition)
+#+ Total number of unique values: 50
 #+ Number of elements in both elixhauser_poa$condition and elixhauser_codes$condition: 37
 #+ Number of elements only in elixhauser_poa$condition: 1
 #+   unique elements: CBVD
-#+ Number of elements only in elixhauser_codes$condition: 11
-#+   unique elements: DRUG_ABUSEPSYCHOSES, CBVD_POA, NEURO_OTH_SEIZ, HFHTN_CX, HTN_CXRENLFL_SEV, HFHTN_CXRENLFL_SEV, CBVD_SQLA, CBVD_SQLAPARALYSIS, ALCOHOLLIVER_MLD, LIVER_MLD_NEURO, VALVE_AUTOIMMUNE
+#+ Number of elements only in elixhauser_codes$condition: 12
+#+   unique elements: DRUG_ABUSEPSYCHOSES, CBVD_POA, NEURO_OTH_SEIZ, HFHTN_CX, HTN_CXRENLFL_SEV, HFHTN_CXRENLFL_SEV, LIVER_MLD_PULMCIRC, CBVD_SQLA, CBVD_SQLAPARALYSIS, ALCOHOLLIVER_MLD, LIVER_MLD_NEURO, VALVE_AUTOIMMUNE
 
 elixhauser_poa <-
   rbind(
@@ -302,9 +323,16 @@ elixhauser_poa <-
     elixhauser_poa[condition == "HF"][, condition := "HFHTN_CXRENLFL_SEV"],
     elixhauser_poa[condition == "NEURO_OTH"][, condition := "NEURO_OTH_SEIZ"],
     elixhauser_poa[condition == "AUTOIMMUNE"][, condition := "VALVE_AUTOIMMUNE"],
-    elixhauser_poa[condition == "LIVER_MLD"][, condition := "LIVER_MLD_NEURO"]
+    elixhauser_poa[condition == "LIVER_MLD"][, condition := "LIVER_MLD_NEURO"],
+    elixhauser_poa[condition == "LIVER_MLD"][, condition := "LIVER_MLD_PULMCIRC"]
   )
 
+#> qwraps2::set_diff(elixhauser_poa$condition, elixhauser_codes$condition)
+#+ Total number of unique values: 50
+#+ Number of elements in both elixhauser_poa$condition and elixhauser_codes$condition: 49
+#+ Number of elements only in elixhauser_poa$condition: 1
+#+   unique elements: CBVD
+#+ Number of elements only in elixhauser_codes$condition: 0
 
 # Under the assumption that the POA required flag is static over the years, then
 # the this data structure is not needed and a POA required flag cold just be

tests/build-expected-ahrq-results/.gitignore

@@ -1 +1,2 @@
 *.sas
+*.csv