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#' Generate \code{vermont_dx} data
#'
#' Process data from \href{healthvermont.gov}{Health Vermont}
#' @template parse-template
#' @examples
#' \dontrun{
#' generate_vermont_dx(save_pkg_data = TRUE)
#' }
#' @keywords internal datagen
#' @noRd
.generate_vermont_dx <- function(save_pkg_data) {
# This is indeed in data-raw, because not available to download anymore
vermont_fp <- .get_raw_data_path("VTINP13.TXT")
vermont_dx <- utils::read.csv(vermont_fp,
stringsAsFactors = FALSE,
strip.white = TRUE
)
vermont_dx <- vermont_dx[1:1000, c(74, 4, 6, 7, 11, 13:32)]
age_group <- vermont_dx$intage
attr(age_group, "class") <- "factor"
attr(age_group, "levels") <- c(
"Under 1", "1-17", "18-24",
"25-29", "30-34", "35-39",
"40-44", "45-49", "50-54",
"55-59", "60-64", "65-69",
"70-74", "75 and over",
"Unknown"
)
age_group <- ordered(age_group)
sex <- vermont_dx$sex
attr(sex, "class") <- "factor"
attr(sex, "levels") <- c("male", "female", "unknown")
vermont_dx$intage <- age_group
vermont_dx$sex <- sex
# death = 8 (other codes are for various discharge statuses)
vermont_dx$dstat <- vermont_dx$dstat == 8
names(vermont_dx)[seq_len(5)] <- c(
"visit_id",
"age_group",
"sex",
"death",
"DRG"
)
class(vermont_dx) <- c("icd_wide_data", "data.frame")
dx_cols <- paste0("DX", seq_len(20))
for (dc in dx_cols) {
class(vermont_dx[[dc]]) <- c("icd9cm", "icd9", "character")
attr(vermont_dx[[dc]], "icd_short_diag") <- TRUE
}
if (save_pkg_data) .save_in_data_dir(vermont_dx)
invisible(vermont_dx)
}
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