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resistance predict

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dr. M.S. (Matthijs) Berends
2019-01-15 12:45:24 +01:00
parent cda7087722
commit 046d195064
16 changed files with 306 additions and 209 deletions
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27
R/first_isolate.R
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@ -23,7 +23,7 @@
#'
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
#' @param tbl a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.
@ -187,9 +187,8 @@ first_isolate <- function(tbl,
# try to find columns based on type
# -- mo
if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
message(blue(paste0("NOTE: Using column `", bold(col_mo), "` as input for `col_mo`.")))
if (is.null(col_mo)) {
col_mo <- search_type_in_df(tbl = tbl, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
@ -197,33 +196,25 @@ first_isolate <- function(tbl,
# -- date
if (is.null(col_date)) {
for (i in 1:ncol(tbl)) {
if ("Date" %in% class(tbl %>% pull(i)) | "POSIXct" %in% class(tbl %>% pull(i))) {
col_date <- colnames(tbl)[i]
message(blue(paste0("NOTE: Using column `", bold(col_date), "` as input for `col_date`.")))
break
}
}
col_date <- search_type_in_df(tbl = tbl, type = "date")
}
if (is.null(col_date)) {
stop("`col_date` must be set.", call. = FALSE)
}
# convert to Date (pipes for supporting tibbles too)
# convert to Date (pipes/pull for supporting tibbles too)
tbl[, col_date] <- tbl %>% pull(col_date) %>% as.Date()
# -- patient id
if (is.null(col_patient_id) & any(colnames(tbl) %like% "^(patient|patid)")) {
col_patient_id <- colnames(tbl)[colnames(tbl) %like% "^(patient|patid)"][1]
message(blue(paste0("NOTE: Using column `", bold(col_patient_id), "` as input for `col_patient_id`.")))
if (is.null(col_patient_id)) {
col_patient_id <- search_type_in_df(tbl = tbl, type = "patient_id")
}
if (is.null(col_patient_id)) {
stop("`col_patient_id` must be set.", call. = FALSE)
}
# -- key antibiotics
if (is.null(col_keyantibiotics) & any(colnames(tbl) %like% "^key.*(ab|antibiotics)")) {
col_keyantibiotics <- colnames(tbl)[colnames(tbl) %like% "^key.*(ab|antibiotics)"][1]
message(blue(paste0("NOTE: Using column `", bold(col_keyantibiotics), "` as input for `col_keyantibiotics`. Use ", bold("col_keyantibiotics = FALSE"), " to prevent this.")))
if (is.null(col_keyantibiotics)) {
col_keyantibiotics <- search_type_in_df(tbl = tbl, type = "keyantibiotics")
}
if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL