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WHONET/EARS-Net support

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dr. M.S. (Matthijs) Berends
2019-01-29 00:06:50 +01:00
parent f6336fdd89
commit 6aae206320
83 changed files with 1428 additions and 633 deletions
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29
R/guess_ab_col.R
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@ -21,7 +21,7 @@
#' Guess antibiotic column
#'
#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
#' @param tbl a \code{data.frame}
#' @param col a character to look for
#' @param verbose a logical to indicate whether additional info should be printed
@ -40,6 +40,16 @@
#' guess_ab_col(df, "J01AA07", verbose = TRUE)
#' # using column `tetr` for col "J01AA07"
#' # [1] "tetr"
#'
#' # WHONET codes
#' df <- data.frame(AMP_ND10 = "R",
#' AMC_ED20 = "S")
#' guess_ab_col(df, "ampicillin")
#' # [1] "AMP_ND10"
#' guess_ab_col(df, "J01CR02")
#' # [1] "AMC_ED20"
#' guess_ab_col(df, as.atc("augmentin"))
#' # [1] "AMC_ED20"
guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (is.null(tbl) & is.null(col)) {
return(as.name("guess_ab_col"))
@ -54,6 +64,11 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
}
tbl_names <- colnames(tbl)
tbl_names_stripped <- colnames(tbl) %>%
strsplit("_") %>%
lapply(function(x) {x[1]}) %>%
unlist()
if (col %in% tbl_names) {
return(col)
}
@ -70,6 +85,15 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
filter_all(any_vars(. %in% tbl_names))
}
# WHONET
if (nrow(ab_result) == 0) {
# use like when col >= 5 characters
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
filter_all(any_vars(tolower(.) == tolower(col))) %>%
filter_all(any_vars(. %in% tbl_names_stripped))
}
if (nrow(ab_result) > 1) {
# looking more and more for reliable hit
ab_result_1 <- ab_result %>% filter(tolower(atc) == tolower(col))
@ -95,6 +119,9 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
return(NULL)
} else {
result <- tbl_names[tbl_names %in% ab_result]
if (length(result) == 0) {
result <- tbl_names[tbl_names_stripped %in% ab_result]
}
if (length(result) == 0) {
if (verbose == TRUE) {
message('no result found for col "', col, '"')