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WHONET fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-03-09 08:21:00 +01:00
parent 0c0c6e289b
commit b319b89750
10 changed files with 80 additions and 68 deletions
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10
R/mo.R
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@ -122,6 +122,7 @@
#' @importFrom dplyr %>% pull left_join
#' @examples
#' # These examples all return "B_STPHY_AUR", the ID of S. aureus:
#' as.mo("sau") # WHONET code
#' as.mo("stau")
#' as.mo("STAU")
#' as.mo("staaur")
@ -598,6 +599,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
# TRY OTHER SOURCES ----
# WHONET and other common LIS codes
if (toupper(x_backup[i]) %in% AMR::microorganisms.codes[, 1]) {
mo_found <- AMR::microorganisms.codes[toupper(x_backup[i]) == AMR::microorganisms.codes[, 1], "mo"][1L]
if (length(mo_found) > 0) {
@ -606,6 +608,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
}
if (!is.null(reference_df)) {
# self-defined reference
if (x_backup[i] %in% reference_df[, 1]) {
ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"]
if (ref_mo %in% microorganismsDT[, mo]) {
@ -617,6 +620,13 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
}
# allow no codes less than 4 characters long, was already checked for WHONET above
if (nchar(x_trimmed[i]) < 4) {
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
failures <- c(failures, x_backup[i])
next
}
check_per_prevalence <- function(data_to_check,
a.x_backup,
b.x_trimmed,