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(v0.7.1.9084) CI fix
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9
R/mo.R
9
R/mo.R
@ -652,9 +652,9 @@ exec_as.mo <- function(x,
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if (!is.null(reference_df)) {
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# self-defined reference
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if (x_backup[i] %in% reference_df[, 1]) {
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ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"]
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if (ref_mo %in% data_to_check[, mo]) {
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x[i] <- data_to_check[mo == ref_mo, ..property][[1]][1L]
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ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"][[1L]]
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if (ref_mo %in% microorganismsDT[, mo]) {
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x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
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next
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} else {
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warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
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@ -769,8 +769,7 @@ exec_as.mo <- function(x,
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}
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next
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}
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if (toupper(x_backup_without_spp[i]) == 'CRS'
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| toupper(x_backup_without_spp[i]) == 'CRSM') {
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if (toupper(x_backup_without_spp[i]) == 'CRSM') {
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# co-trim resistant S. maltophilia
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x[i] <- microorganismsDT[mo == 'B_STNTR_MLTP', ..property][[1]][1L]
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if (initial_search == TRUE) {
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