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improve hcc function input error checking
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rename variables to match style
update example
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@anobel
anobel committed May 2, 2016
1 parent 959c6df commit 80b5b5f
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Showing 3 changed files with 50 additions and 34 deletions.
64 changes: 36 additions & 28 deletions R/comorbid.R
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,12 @@ icd9PoaChoices <- icd_poa_choices
#' pts <- icd_long_data(visit_name = c("2", "1", "2", "3", "3"),
#' icd9 = c("39891", "40110", "09322", "41514", "39891"))
#' icd_comorbid(pts, icd9_map_ahrq, short_code = TRUE) # visit_name is now sorted
#' pt_hccs <- icd_comorbid_hcc(ptdata, date)
#' pts <- icd_long_data(
#' visit_name = c("2", "1", "2", "3", "3"),
#' icd9 = c("20084", "1742", "30410", "41514", "95893"),
#' date = as.Date(c("2011-01-01", "2011-05-01", "2011-03-01",
#' "2011-02-01", "2011-02-01")))
#' pt_hccs <- icd_comorbid_hcc(pts, visit_date="date")

#' @export
icd_comorbid <- function(x, map, ...) {
Expand Down Expand Up @@ -593,21 +598,22 @@ icd10_comorbid_quan_deyo <- function(x, ..., abbrev_names = TRUE, hierarchy = TR
#' @rdname icd_comorbid
#' @export
icd9_comorbid_hcc <- function(x,
visit_name=NULL,
icd_name = NULL,
date = "date") {
visit_date = "date",
visit_name = NULL,
icd_name = NULL
) {
assert_data_frame(x, min.cols = 3, col.names = "unique")
assert(checkString(visit_name), checkNull(visit_name))
assert(checkString(icd_name), checkNull(icd_name))
visit_name <- get_visit_name(x, visit_name)
icd_name <- get_icd_name(x, icd_name)
assert_string(visit_date)
assert_string(visit_name)
assert_string(icd_name)

icd_map <- icd::icd9_map_cc
# Convert date and add column for year
x[[date]] <- as.Date(x[[date]])
x$year <- as.numeric(format(x[[date]], "%Y"))
# Add column for year
x$year <- as.numeric(format(x[[visit_date]], "%Y"))

# merge CCs to patient data based on ICD and year drop ICD info
x <- merge(x, icd_map, all.x = T)
Expand All @@ -617,16 +623,16 @@ icd9_comorbid_hcc <- function(x,
x <- x[!is.na(x$cc), ]
x$cc <- as.numeric(x$cc)

# keep id, admtdate, and cc columns only, reorder
x <- x[, c("id", date, "year", "cc")]
# keep id, date, and cc columns only, reorder
x <- x[, c(visit_name, visit_date, "year", "cc")]

# Keep only unique records
# Multiple ICDs for a patient can resolve to same CC
x <- unique(x)

# Import hierarchy mappings, and duplicate the ifcc column
# needed for future matching
hierarchy <- icd::icd_map_cc_hcc
hierarchy <- icd_map_cc_hcc
hierarchy$cc <- hierarchy$ifcc

# Merge hierarchy rules with patient data
Expand All @@ -642,7 +648,7 @@ icd9_comorbid_hcc <- function(x,
# Rename all dataframes in list to same column names
# rbind into a single dataframe
todrop <- lapply(1:length(todrop), function(x) {
names(todrop[[x]]) <- c("id", date, "cc")
names(todrop[[x]]) <- c(visit_name, visit_date, "cc")
return(todrop[[x]])
}
)
Expand All @@ -660,54 +666,55 @@ icd9_comorbid_hcc <- function(x,

# Drop flagged patients and keep columns of interest
x <- x[is.na(x$todrop), ]
x <- x[, c("id", date, "cc")]
names(x) <- c("id", date, "hcc")
x <- x[, c(visit_name, visit_date, "cc")]
names(x) <- c(visit_name, visit_date, "hcc")
return(x)
}

#' @rdname icd_comorbid
#' @export
icd10_comorbid_hcc <- function(x,
visit_name=NULL,
icd_name = NULL,
date = "date") {
visit_date = "date",
visit_name = NULL,
icd_name = NULL
) {
assert_data_frame(x, min.cols = 3, col.names = "unique")
assert(checkString(visit_name), checkNull(visit_name))
assert(checkString(icd_name), checkNull(icd_name))
visit_name <- get_visit_name(x, visit_name)
icd_name <- get_icd_name(x, icd_name)
assert_string(visit_date)
assert_string(visit_name)
assert_string(icd_name)

icd_map <- icd::icd10_map_cc
# Convert date and add column for year
x[[date]] <- as.Date(x[[date]])
x$year <- as.numeric(format(x[[date]], "%Y"))
# Add column for year
x$year <- as.numeric(format(x[[visit_date]], "%Y"))

# merge CCs to patient data based on ICD and year drop ICD info
x <- merge(x, icd_map, all.x = T)

# Drop missing CC and convert to numeric
# as not all ICDs resolve to a CC by definition
# Not all ICDs resolve to a CC by definition
x <- x[!is.na(x$cc), ]
x$cc <- as.numeric(x$cc)

# keep id, admtdate, and cc columns only, reorder
x <- x[, c("id", date, "year", "cc")]
# keep id, date, and cc columns only, reorder
x <- x[, c(visit_name, visit_date, "year", "cc")]

# Keep only unique records
# multiple ICDs for a patient can resolve to same CC
# Multiple ICDs for a patient can resolve to same CC
x <- unique(x)

# Import hierarchy mappings, and duplicate the ifcc column
# needed for future matching
hierarchy <- icd::icd_map_cc_hcc
hierarchy <- icd_map_cc_hcc
hierarchy$cc <- hierarchy$ifcc

# Merge hierarchy rules with patient data
x <- merge(x, hierarchy, all.x = TRUE)

# Create a list of dataframes that contain the CCs that will be zero'd out
# Create a list of dataframes that contain the CCs that will be zeroed out
todrop <- list()
for (i in 1:6) {
todrop[[i]] <- x[!is.na(x$ifcc), c(3, 4, 5 + i)]
Expand All @@ -717,7 +724,7 @@ icd10_comorbid_hcc <- function(x,
# Rename all dataframes in list to same column names
# rbind into a single dataframe
todrop <- lapply(1:length(todrop), function(x) {
names(todrop[[x]]) <- c("id", date, "cc")
names(todrop[[x]]) <- c(visit_name, visit_date, "cc")
return(todrop[[x]])
}
)
Expand All @@ -735,10 +742,11 @@ icd10_comorbid_hcc <- function(x,

# Drop flagged patients and keep columns of interest
x <- x[is.na(x$todrop), ]
x <- x[, c("id", date, "cc")]
names(x) <- c("id", date, "hcc")
x <- x[, c(visit_name, visit_date, "cc")]
names(x) <- c(visit_name, visit_date, "hcc")
return(x)
}

#' @rdname icd_comorbid
#' @export
icd_comorbid_ahrq <- function(x, icd_name = get_icd_name(x), ...) {
Expand Down
3 changes: 2 additions & 1 deletion man/icd9_parse_cc.Rd
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17 changes: 12 additions & 5 deletions man/icd_comorbid.Rd
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1 comment on commit 80b5b5f

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R/comorbid.R:635:16: warning: no visible binding for global variable ‘icd_map_cc_hcc’

​  hierarchy <- icd_map_cc_hcc
               ^~~~~~~~~~~~~~

R/comorbid.R:711:16: warning: no visible binding for global variable ‘icd_map_cc_hcc’

​  hierarchy <- icd_map_cc_hcc
               ^~~~~~~~~~~~~~

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