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(v2.1.1.9260) fix antibiogram

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dr. M.S. (Matthijs) Berends
2025-04-29 16:15:18 +02:00
parent 6819473457
commit faa9ae0d85
31 changed files with 195 additions and 2283 deletions
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54
R/sir.R
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@ -729,7 +729,7 @@ as.sir.data.frame <- function(x,
# -- MO
col_mo.bak <- col_mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
}
# -- host
@ -742,7 +742,7 @@ as.sir.data.frame <- function(x,
}
if (breakpoint_type == "animal") {
if (is.null(host)) {
host <- search_type_in_df(x = x, type = "host", add_col_prefix = FALSE)
host <- search_type_in_df(x = x, type = "host", add_col_prefix = FALSE, info = info)
} else if (length(host) == 1 && as.character(host) %in% colnames(x)) {
host <- x[[as.character(host)]]
}
@ -753,7 +753,7 @@ as.sir.data.frame <- function(x,
# -- UTIs
col_uti <- uti
if (is.null(col_uti)) {
col_uti <- search_type_in_df(x = x, type = "uti", add_col_prefix = FALSE)
col_uti <- search_type_in_df(x = x, type = "uti", add_col_prefix = FALSE, info = info)
}
if (!is.null(col_uti)) {
if (is.logical(col_uti)) {
@ -773,7 +773,7 @@ as.sir.data.frame <- function(x,
}
} else {
# col_uti is still NULL - look for specimen column and make logicals of the urines
col_specimen <- suppressMessages(search_type_in_df(x = x, type = "specimen"))
col_specimen <- suppressMessages(search_type_in_df(x = x, type = "specimen", info = info))
if (!is.null(col_specimen)) {
uti <- x[, col_specimen, drop = TRUE] %like% "urin"
values <- sort(unique(x[uti, col_specimen, drop = TRUE]))
@ -846,7 +846,7 @@ as.sir.data.frame <- function(x,
stop_if(is.null(col_mo), "`col_mo` must be set")
# if not null, we already found it, now find again so a message will show
if (is.null(col_mo.bak)) {
col_mo <- search_type_in_df(x = x, type = "mo")
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
}
x_mo <- as.mo(x[, col_mo, drop = TRUE], info = info)
}
@ -854,10 +854,17 @@ as.sir.data.frame <- function(x,
# set up parallel computing
n_cores <- get_n_cores(max_cores = max_cores)
n_cores <- min(n_cores, length(ab_cols)) # never more cores than variables required
if (isTRUE(parallel) && .Platform$OS.type != "windows" && getRversion() < "4.0.0") {
n_cores <- 1
if (isTRUE(info)) {
warning("Parallel computing is not available on unix in R < 4.0", call. = FALSE)
if (isTRUE(parallel) && (.Platform$OS.type == "windows" || getRversion() < "4.0.0")) {
cl <- tryCatch(parallel::makeCluster(n_cores, type = "PSOCK"),
error = function(e) {
if (isTRUE(info)) {
message_("Could not create parallel cluster, using single-core computation. Error message: ", e$message, add_fn = font_red)
}
return(NULL)
}
)
if (is.null(cl)) {
n_cores <- 1
}
}
@ -959,10 +966,10 @@ as.sir.data.frame <- function(x,
if (isTRUE(parallel) && n_cores > 1 && length(ab_cols) > 1) {
if (isTRUE(info)) {
message()
message_("Running in parallel mode using ", n_cores, " out of ", get_n_cores(Inf), " cores, on columns ", vector_and(font_bold(ab_cols, collapse = NULL), quotes = "'", sort = FALSE), "...", as_note = FALSE, appendLF = FALSE, add_fn = font_red)
message_("Running in parallel mode using ", n_cores, " out of ", get_n_cores(Inf), " cores, on columns ", vector_and(font_bold(ab_cols, collapse = NULL), quotes = "'", sort = FALSE), "...", as_note = FALSE, appendLF = FALSE)
}
if (.Platform$OS.type == "windows" || getRversion() < "4.0.0") {
cl <- parallel::makeCluster(n_cores, type = "PSOCK")
# `cl` has been created in the part above before the `run_as_sir_column` function
on.exit(parallel::stopCluster(cl), add = TRUE)
parallel::clusterExport(cl, varlist = c(
"x", "x.bak", "x_mo", "ab_cols", "types",
@ -974,12 +981,13 @@ as.sir.data.frame <- function(x,
), envir = environment())
result_list <- parallel::parLapply(cl, seq_along(ab_cols), run_as_sir_column)
} else {
# R>=4.0 on unix
result_list <- parallel::mclapply(seq_along(ab_cols), run_as_sir_column, mc.cores = n_cores)
}
if (isTRUE(info)) {
message_(" Done.", appendLF = TRUE, as_note = FALSE, add_fn = font_red)
message_(font_green_bg(" DONE "), as_note = FALSE)
message()
message_("Run `sir_interpretation_history()` to retrieve a logbook with all the details of the breakpoint interpretations.", add_fn = font_green)
message_("Run `sir_interpretation_history()` to retrieve a logbook with all details of the breakpoint interpretations.", add_fn = font_green)
}
} else {
# sequential mode (non-parallel)
@ -1116,7 +1124,7 @@ as_sir_method <- function(method_short,
if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
message()
message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all the details of the breakpoint interpretations.\n\n", add_fn = font_green)
message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n", add_fn = font_green)
}
current_df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
@ -1200,7 +1208,7 @@ as_sir_method <- function(method_short,
mo <- NULL
try(
{
mo <- suppressMessages(search_type_in_df(df, "mo", add_col_prefix = FALSE))
mo <- suppressMessages(search_type_in_df(df, "mo", add_col_prefix = FALSE, info = info))
},
silent = TRUE
)
@ -1236,7 +1244,7 @@ as_sir_method <- function(method_short,
uti <- NULL
try(
{
uti <- suppressMessages(search_type_in_df(df, "uti", add_col_prefix = FALSE))
uti <- suppressMessages(search_type_in_df(df, "uti", add_col_prefix = FALSE, info = info))
},
silent = TRUE
)
@ -1441,14 +1449,7 @@ as_sir_method <- function(method_short,
if (nrow(breakpoints) == 0) {
# apparently no breakpoints found
if (isTRUE(info)) {
message(
paste0(font_rose_bg(" WARNING "), "\n"),
font_black(paste0(
" ", AMR_env$bullet_icon, " No ", method_coerced, " breakpoints available for ",
suppressMessages(suppressWarnings(ab_name(unique(ab_coerced), language = NULL, tolower = TRUE, info = info))),
" (", unique(ab_coerced), ")."
), collapse = "\n")
)
message(font_grey_bg(font_black(" NO BREAKPOINTS ")))
}
load_mo_uncertainties(metadata_mo)
@ -1829,12 +1830,13 @@ as_sir_method <- function(method_short,
message(font_yellow_bg(" NOTE "))
}
notes <- unique(notes)
if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
# if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
if (isTRUE(verbose)) {
for (i in seq_along(notes)) {
message(word_wrap(" ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
}
} else {
message(word_wrap(" ", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
# message(word_wrap(" ", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
}
} else {
message(font_green_bg(" OK "))