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dewittpe merged 2 commits into from
Nov 18, 2025
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Fix 16 #23

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156f816
fix #16
dewittpe Nov 18, 2025
af10df4
update vignettes to account for primarydx expectations for charlson; …
dewittpe Nov 18, 2025
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10 changes: 8 additions & 2 deletions R/charlson.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
#' @param iddf A `data.frame` of unique IDs
#' @param cmrb A `data.frame` containing at least `id.vars` and
#' `condition` columns; i.e., the 'comorbidity' `data.frame`.
#' @param primarydx.var Character (scalar) with the name of the column in
#' `cmrb` denoting if the condition was flaged as a primary diagnostic or not.
#' @param method Character scalar; name of the Charlson variant to assess
#'
#' @return A `data.frame` with `id.vars`, per-condition 0/1
Expand All @@ -15,8 +17,12 @@
#' @family internal comorbidity functions
#' @noRd
#' @keywords internal
.charlson <- function(id.vars, iddf, cmrb, method) {
ccc <- unique(mdcr_select(cmrb, cols = c(id.vars, "condition")))
.charlson <- function(id.vars, iddf, cmrb, primarydx.var, method) {
ccc <- unique(mdcr_select(cmrb, cols = c(id.vars, "condition", primarydx.var)))

# omit primary dx
idx <- which(ccc[[primarydx.var]] == 0L)
ccc <- mdcr_subset(ccc, i = idx)

# get the method weights and conditions
conditions <- mdcr_subset(..mdcr_internal_charlson_index_scores..,
Expand Down
28 changes: 16 additions & 12 deletions R/comorbidities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,7 @@ comorbidities.data.frame <- function(data,
}
}

if (startsWith(method, "elixhauser") & !is.null(primarydx.var)) {
if ((startsWith(method, "elixhauser") | startsWith(method, "charlson")) & !is.null(primarydx.var)) {
is_a_column(primarydx.var, names(data))
pn <- primarydx.var %in% ..protected_names..
if (pn) {
Expand All @@ -268,6 +268,9 @@ comorbidities.data.frame <- function(data,
)
)
}
} else if (startsWith(method, "pccc") & (!is.null(primarydx.var) | !is.null(primarydx))) {
warning("primarydx.var and primarydx are ignored when method = '%s'", method)
primarydx.var <- primarydx <- NULL
}

flag.method <-
Expand Down Expand Up @@ -447,26 +450,22 @@ comorbidities.data.frame <- function(data,
is_a_column(poa.var, nms)
}

if (startsWith(method, "elixhauser")) {
if (startsWith(method, "elixhauser") | startsWith(method, "charlson")) {
if (is.null(primarydx.var)) {
if (!is.null(primarydx)) {
stopifnot(inherits(primarydx, "numeric") | inherits(primarydx, "integer"))
stopifnot(length(primarydx) == 1L)
primarydx <- as.integer(primarydx)
stopifnot(primarydx %in% c(0L, 1L))
} else {
if (grepl("^elixhauser", method)) {
warning("Assuming all codes provided are secondary diagnostic codes. Define `primarydx.var` or `primarydx` if this assumption is incorrect.", call. = FALSE)
}
warning("Assuming all codes provided are secondary diagnostic codes. Define `primarydx.var` or `primarydx` if this assumption is incorrect.", call. = FALSE)
primarydx <- 0L
}

primarydx.var <- build_name("..medicalcoder_primarydx..", nms)

if (grepl("^elixhauser", method)) {
on_full <- mdcr_set(on_full, j = primarydx.var, value = rep(primarydx, nrow(on_full)))
on_comp <- mdcr_set(on_comp, j = primarydx.var, value = rep(primarydx, nrow(on_comp)))
}
on_full <- mdcr_set(on_full, j = primarydx.var, value = rep(primarydx, nrow(on_full)))
on_comp <- mdcr_set(on_comp, j = primarydx.var, value = rep(primarydx, nrow(on_comp)))

} else {
if (!is.null(primarydx)) {
Expand Down Expand Up @@ -556,7 +555,12 @@ comorbidities.data.frame <- function(data,

cmrb <- do.call(rbind, foc)

cmrb[[poa.var]][cmrb[[encid]] > cmrb[["first_occurrance"]]] <- 1L
# set poa to 1 and primarydx to 0 for prior conditions
idx <- cmrb[[encid]] > cmrb[["first_occurrance"]]
cmrb[[poa.var]][idx] <- 1L
if (!is.null(primarydx.var)) {
cmrb[[primarydx.var]][cmrb[[encid]] > cmrb[["first_occurrance"]]] <- 0L
}
cmrb <- mdcr_set(cmrb, j = "first_occurrance", value = NULL)

cmrb <- unique(cmrb)
Expand All @@ -577,7 +581,7 @@ comorbidities.data.frame <- function(data,
} else if (startsWith(method, "pccc_v3")) {
ccc <- .pccc_v3(id.vars = id.vars, iddf = iddf, cmrb = cmrb, subconditions = subconditions)
} else if (startsWith(method, "charlson")) {
ccc <- .charlson(id.vars = id.vars, iddf = iddf, cmrb = cmrb, method)
ccc <- .charlson(id.vars = id.vars, iddf = iddf, cmrb = cmrb, primarydx.var = primarydx.var, method = method)
if (!is.null(age.var)) {
ages <- unique(mdcr_select(data, cols = c(id.vars, age.var)))
ages[["age_score"]] <- as.integer(cut(ages[[age.var]], breaks = c(-Inf, 50, 60, 70, 80, Inf), right = FALSE)) - 1L
Expand All @@ -587,7 +591,7 @@ comorbidities.data.frame <- function(data,
ccc[["age_score"]] <- rep(NA_integer_, nrow(ccc))
}
} else if (startsWith(method, "elixhauser")) {
ccc <- .elixhauser(id.vars = id.vars, iddf = iddf, cmrb = cmrb, poa.var = poa.var, primarydx.var = primarydx.var, method)
ccc <- .elixhauser(id.vars = id.vars, iddf = iddf, cmrb = cmrb, poa.var = poa.var, primarydx.var = primarydx.var, method = method)
} else {
stop(sprintf("method '%s' has not yet been implemented", method))
}
Expand Down
6 changes: 3 additions & 3 deletions man-roxygen/params-comorbidities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,9 @@
#'
#' @param primarydx.var Character scalar naming the column in `data` that
#' indicates whether `data[[icd.codes]]` are primary diagnostic codes (`1L`)
#' or not (`0L`). Primary diagnosis is used only for Elixhauser comorbidities
#' and is ignored when the method is PCCC or Charlson. `primarydx.var` takes
#' precedence over `primarydx` if both are provided.
#' or not (`0L`). Primary diagnosis is used only for Elixhauser and Charlson
#' comorbidities and is ignored when the method is a PCCC variant.
#' `primarydx.var` takes precedence over `primarydx` if both are provided.
#'
#' @param primarydx An integer value of `0` or `1`. If `0`,
#' treat all codes as non-primary diagnoses; if `1`, treat all codes as
Expand Down
6 changes: 3 additions & 3 deletions man/comorbidities.Rd
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15 changes: 15 additions & 0 deletions tests/test-comorbidities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,21 @@ stopifnot(
inherits(out4, "error")
)

################################################################################
# when a primarydx.var was passed to comorbidities when not needed an error was
# thrown. https://github.com/dewittpe/medicalcoder/issues/16
#
# This has been corrected to be a warning - ignore primarydx.var unless
# elixhauser_ahrq2022 or newer
comorbidities(
data = mdcr,
id.var = "patid",
#primarydx.var = "full_code",
method = "charlson_quan2005",
icd.codes = "code",
poa = 1
)

################################################################################
# End of File #
################################################################################
1 change: 1 addition & 0 deletions vignettes/charlson.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,7 @@ mdcr_results <-
dx.var = "dx",
flag.method = "current",
poa = 1,
primarydx = 0,
method = "charlson_quan2005"
)
```
Expand Down
50 changes: 25 additions & 25 deletions vignettes/comorbidities.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,7 @@ subset(
record <-
structure(
list(
patid = c("A", "A", "A", "A", "A", "A", "A"),
patid = c("A", "A", "A", "A", "A", "A", "A"),
encid = c(1L, 2L, 3L, 4L, 5L, 5L, 6L),
code = c(NA, "C78.4", "I50.40", NA, "C78.4", "I50.40", NA),
poa = c(NA, 0L, 1L, NA, 1L, 0L, NA)),
Expand All @@ -236,12 +236,11 @@ args <-
icd.codes = "code",
id.vars = c("patid", "encid"),
icdv = 10L,
dx = 1,
primarydx = 0L
dx = 1
)
args_current_poa0 <- c(args, poa = 0L, flag.method = "current")
args_current_poa1 <- c(args, poa = 1L, flag.method = "current")
args_current_poav <- c(args, poa.var = "poa", flag.method = "current")
args_current_poa0 <- c(args, poa = 0L, flag.method = "current")
args_current_poa1 <- c(args, poa = 1L, flag.method = "current")
args_current_poav <- c(args, poa.var = "poa", flag.method = "current")
args_cumulative_poa0 <- c(args, poa = 0L, flag.method = "cumulative")
args_cumulative_poa1 <- c(args, poa = 1L, flag.method = "cumulative")
args_cumulative_poav <- c(args, poa.var = "poa", flag.method = "cumulative")
Expand All @@ -256,29 +255,29 @@ rtn <-
do.call(cbind,
list(
left_cols,
do.call(comorbidities, c(args_current_poa0, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_current_poa0, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_current_poa0, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_current_poa1, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_current_poa1, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_current_poa1, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_current_poav, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_current_poav, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_current_poav, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)]
do.call(comorbidities, c(args_current_poa0, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_current_poa0, primarydx = 0L, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_current_poa0, primarydx = 0L, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_current_poa1, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_current_poa1, primarydx = 0L, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_current_poa1, primarydx = 0L, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_current_poav, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_current_poav, primarydx = 0L, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_current_poav, primarydx = 0L, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)]
))
,
do.call(cbind,
list(
left_cols,
do.call(comorbidities, c(args_cumulative_poa0, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_cumulative_poa0, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_cumulative_poa0, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_cumulative_poa1, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_cumulative_poa1, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_cumulative_poa1, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_cumulative_poav, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_cumulative_poav, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_cumulative_poav, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)]
do.call(comorbidities, c(args_cumulative_poa0, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_cumulative_poa0, primarydx = 0L, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_cumulative_poa0, primarydx = 0L, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_cumulative_poa1, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_cumulative_poa1, primarydx = 0L, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_cumulative_poa1, primarydx = 0L, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)],
do.call(comorbidities, c(args_cumulative_poav, method = "pccc_v3.0"))[, .(CVD = cvd_dxpr_or_tech, CANCER = malignancy_dxpr_or_tech)],
do.call(comorbidities, c(args_cumulative_poav, primarydx = 0L, method = "charlson_quan2011"))[, .(CVD = chf, CANCER = mst)],
do.call(comorbidities, c(args_cumulative_poav, primarydx = 0L, method = "elixhauser_ahrq2025"))[, .(CVD = HF, CANCER = CANCER_METS)]
))
)
```
Expand Down Expand Up @@ -366,7 +365,8 @@ cmdf_mdcr <-
dx.var = "dx",
method = "charlson_cdmf2019",
flag.method = "current",
poa = 1)
primarydx = 0L,
poa = 1L)
data.table::setDT(cmdf_mdcr)

cmdf_mdcr[, .N, keyby = .(hiv, aids)]
Expand Down