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mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:11:54 +02:00

(v0.7.1.9084) CI fix

This commit is contained in:
2019-09-23 20:55:54 +02:00
parent 8ce252fbc5
commit 76dc948067
12 changed files with 61 additions and 64 deletions

9
R/mo.R
View File

@ -652,9 +652,9 @@ exec_as.mo <- function(x,
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% data_to_check[, mo]) {
x[i] <- data_to_check[mo == ref_mo, ..property][[1]][1L]
ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"][[1L]]
if (ref_mo %in% microorganismsDT[, mo]) {
x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
next
} else {
warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
@ -769,8 +769,7 @@ exec_as.mo <- function(x,
}
next
}
if (toupper(x_backup_without_spp[i]) == 'CRS'
| toupper(x_backup_without_spp[i]) == 'CRSM') {
if (toupper(x_backup_without_spp[i]) == 'CRSM') {
# co-trim resistant S. maltophilia
x[i] <- microorganismsDT[mo == 'B_STNTR_MLTP', ..property][[1]][1L]
if (initial_search == TRUE) {