P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 07:51:57 +02:00
Code Releases Activity

(v0.8.0.9004) added MDR guideline by Magiorakos et al.

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-10-26 21:56:41 +02:00
parent c01dc8a5b7
commit d2e8249edd
20 changed files with 605 additions and 118 deletions
Download Patch File Download Diff File Expand all files Collapse all files

30
R/guess_ab_col.R
View File

@ -166,26 +166,31 @@ get_column_abx <- function(x,
# sort on name
x <- x[order(names(x), x)]
duplicates <- x[base::duplicated(x)]
x <- x[!names(x) %in% names(duplicates)]
duplicates <- c(x[base::duplicated(x)], x[base::duplicated(names(x))])
duplicates <- duplicates[unique(names(duplicates))]
x <- c(x[!names(x) %in% names(duplicates)], duplicates)
x <- x[order(names(x), x)]
# succeeded with aut-guessing
message(blue("OK."))
if (verbose == TRUE) {
for (i in seq_len(length(x))) {
for (i in seq_len(length(x))) {
if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), ").")))
}
} else if (length(duplicates) > 0) {
for (i in seq_len(length(duplicates))) {
warning(red(paste0("Using column `", bold(duplicates[i]), "` as input for `", names(x[which(x == duplicates[i])]),
"` (", ab_name(names(x[names(which(x == duplicates))[i]]), tolower = TRUE),
"), although it was matched for multiple antibiotics or columns.")), call. = FALSE)
if (names(x[i]) %in% names(duplicates)) {
warning(red(paste0("Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE),
"), although it was matched for multiple antibiotics or columns.")),
call. = FALSE,
immediate. = verbose)
}
}
if (!is.null(hard_dependencies)) {
hard_dependencies <- unique(hard_dependencies)
if (!all(hard_dependencies %in% names(x))) {
# missing a hard dependency will return NA and consequently the data will not be analysed
missing <- hard_dependencies[!hard_dependencies %in% names(x)]
@ -194,6 +199,7 @@ get_column_abx <- function(x,
}
}
if (!is.null(soft_dependencies)) {
soft_dependencies <- unique(soft_dependencies)
if (!all(soft_dependencies %in% names(x))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
@ -203,7 +209,7 @@ get_column_abx <- function(x,
mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
arrange(missing_names) %>%
pull(txt)
message(blue("NOTE: Reliability might be improved if these antimicrobial results would be available too:",
message(blue("NOTE: Reliability will be improved if these antimicrobial results would be available too:",
paste(missing_txt, collapse = ", ")))
}
}