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expert rules 12.0

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dr. M.S. (Matthijs) Berends
2022-11-14 15:20:39 +01:00
parent 7ca44fb756
commit f6862a139d
35 changed files with 433 additions and 128 deletions
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22
R/guess_ab_col.R
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@ -77,7 +77,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
ab_result <- unname(all_found[names(all_found) == search_string.ab])
if (length(ab_result) == 0) {
if (verbose == TRUE) {
if (isTRUE(verbose)) {
message_("No column found as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
add_fn = font_black,
@ -86,7 +86,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
}
return(NULL)
} else {
if (verbose == TRUE) {
if (isTRUE(verbose)) {
message_(
"Using column '", font_bold(ab_result), "' as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ")."
@ -147,7 +147,7 @@ get_column_abx <- function(x,
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
meet_criteria(sort, allow_class = "logical", has_length = 1)
if (info == TRUE) {
if (isTRUE(info)) {
message_("Auto-guessing columns suitable for analysis", appendLF = FALSE, as_note = FALSE)
}
@ -159,14 +159,14 @@ get_column_abx <- function(x,
if (NROW(x) > 10000) {
# only test maximum of 10,000 values per column
if (info == TRUE) {
if (isTRUE(info)) {
message_(" (using only ", font_bold("the first 10,000 rows"), ")...",
appendLF = FALSE,
as_note = FALSE
)
}
x <- x[1:10000, , drop = FALSE]
} else if (info == TRUE) {
} else if (isTRUE(info)) {
message_("...", appendLF = FALSE, as_note = FALSE)
}
@ -210,7 +210,7 @@ get_column_abx <- function(x,
if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (anyNA(newnames)) {
if (info == TRUE) {
if (isTRUE(info)) {
message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
}
warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
@ -221,7 +221,7 @@ get_column_abx <- function(x,
}
unexisting_cols <- which(!vapply(FUN.VALUE = logical(1), dots, function(col) all(col %in% x_columns)))
if (length(unexisting_cols) > 0) {
if (info == TRUE) {
if (isTRUE(info)) {
message_(" ERROR", add_fn = list(font_red, font_bold), as_note = FALSE)
}
stop_("Column(s) not found: ", vector_and(unlist(dots[[unexisting_cols]]), quotes = FALSE),
@ -240,7 +240,7 @@ get_column_abx <- function(x,
}
if (length(out) == 0) {
if (info == TRUE && all_okay == TRUE) {
if (isTRUE(info) && all_okay == TRUE) {
message_("No columns found.")
}
AMR_env$get_column_abx.call <- unique_call_id(entire_session = FALSE, match_fn = fn)
@ -259,14 +259,14 @@ get_column_abx <- function(x,
all_okay <- FALSE
}
if (info == TRUE) {
if (isTRUE(info)) {
if (all_okay == TRUE) {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
} else {
message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
}
for (i in seq_len(length(out))) {
if (verbose == TRUE && !names(out[i]) %in% names(duplicates)) {
if (isTRUE(verbose) && !names(out[i]) %in% names(duplicates)) {
message_(
"Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
@ -304,7 +304,7 @@ get_column_abx <- function(x,
}
if (!is.null(soft_dependencies)) {
soft_dependencies <- unique(soft_dependencies)
if (info == TRUE && !all(soft_dependencies %in% names(out))) {
if (isTRUE(info) && !all(soft_dependencies %in% names(out))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(out)]
missing_msg <- vector_and(paste0(