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(v1.3.0.9002) intrinsic_resistant data set

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dr. M.S. (Matthijs) Berends
2020-08-14 13:36:10 +02:00
parent 7d16bec21f
commit 08d62bb5d5
111 changed files with 50487 additions and 525 deletions
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4
R/guess_ab_col.R
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@ -141,7 +141,7 @@ get_column_abx <- function(x,
x <- x[, x_columns, drop = FALSE] # without drop = TRUE, x will become a vector when x_columns is length 1
df_trans <- data.frame(colnames = colnames(x),
abcode = suppressWarnings(as.ab(colnames(x))))
abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)))
df_trans <- df_trans[!is.na(df_trans$abcode), ]
x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode
@ -150,7 +150,7 @@ get_column_abx <- function(x,
# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
dots <- list(...)
if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots)))
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (any(is.na(newnames))) {
warning("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
call. = FALSE, immediate. = TRUE)