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dr. M.S. (Matthijs) Berends
2026-03-20 15:17:34 +01:00
parent 51f689b069
commit d28671c34d
8 changed files with 94 additions and 92 deletions
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133
R/mo.R
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@@ -267,7 +267,7 @@ as.mo <- function(x,
if (isTRUE(info) && message_not_thrown_before("as.mo", old, new, entire_session = TRUE) && any(is.na(old) & !is.na(new), na.rm = TRUE)) {
message_(
"Returning previously coerced value", ifelse(sum(is.na(old) & !is.na(new)) > 1, "s", ""),
" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this. This note will be shown once per session for this input."
" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run {.help [{.fun mo_reset_session}](AMR::mo_reset_session)} to reset this. This note will be shown once per session for this input."
)
}
@@ -407,7 +407,9 @@ as.mo <- function(x,
paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"),
minimum_matching_score
),
". Try setting this value lower or even to 0.", call = FALSE)
". Try setting this value lower or even to 0.",
call = FALSE
)
result_mo <- NA_character_
} else {
result_mo <- MO_lookup_current$mo[match(top_hits[1], MO_lookup_current$fullname)]
@@ -453,8 +455,8 @@ as.mo <- function(x,
if (length(AMR_env$mo_uncertainties$original_input) <= 3) {
examples <- vector_and(
paste0(
'"', AMR_env$mo_uncertainties$original_input,
'" (assumed ', italicise(AMR_env$mo_uncertainties$fullname), ")"
"{.val ", AMR_env$mo_uncertainties$original_input,
"} (assumed ", italicise(AMR_env$mo_uncertainties$fullname), ")"
),
quotes = FALSE
)
@@ -463,7 +465,7 @@ as.mo <- function(x,
}
msg <- c(msg, paste0(
"Microorganism translation was uncertain for ", examples,
". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add custom entries."
". Run {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to review ", plural[2], ", or use {.help [{.fun add_custom_microorganisms}](AMR::add_custom_microorganisms)} to add custom entries."
))
for (m in msg) {
@@ -479,11 +481,11 @@ as.mo <- function(x,
if (isFALSE(keep_synonyms)) {
out[!is.na(out_current)] <- out_current[!is.na(out_current)]
if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
print(mo_renamed(), extra_txt = " (use {.arg keep_synonyms = TRUE} to leave uncorrected)")
}
} else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
# keep synonyms is TRUE, so check if any do have synonyms
warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use {.arg keep_synonyms = FALSE} to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
}
# Apply Becker ----
@@ -907,14 +909,16 @@ rep.mo <- function(x, ...) {
print.mo_uncertainties <- function(x, n = 10, ...) {
more_than_50 <- FALSE
if (NROW(x) == 0) {
cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n\n")))
message_("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
return(invisible(NULL))
} else if (NROW(x) > 50) {
more_than_50 <- TRUE
x <- x[1:50, , drop = FALSE]
}
cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.\n\n")))
message_("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.",
as_note = FALSE
)
add_MO_lookup_to_AMR_env()
@@ -924,12 +928,13 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
col_green <- function(x) font_green_bg(x, collapse = NULL)
if (has_colour()) {
cat(font_blue(word_wrap("Colour keys: ",
cat(word_wrap(
"Colour keys: ",
col_red(" 0.000-0.549 "),
col_orange(" 0.550-0.649 "),
col_yellow(" 0.650-0.749 "),
col_green(" 0.750-1.000")
)), font_green_bg(" "), "\n", sep = "")
), font_green_bg(" "), "\n", sep = "")
}
score_set_colour <- function(text, scores) {
@@ -960,21 +965,6 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
# sort on descending scores
candidates_formatted <- candidates_formatted[order(1 - scores)]
scores_formatted <- scores_formatted[order(1 - scores)]
candidates <- word_wrap(
paste0(
"Also matched: ",
vector_and(
paste0(
candidates_formatted,
font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
),
quotes = FALSE, sort = FALSE
)
),
extra_indent = nchar("Also matched: "),
width = 0.9 * getOption("width", 100)
)
} else {
candidates <- ""
}
@@ -984,46 +974,54 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
n = x[i, ]$fullname
)
score_formatted <- trimws(formatC(round(score, 3), format = "f", digits = 3))
txt <- paste(txt,
out <- paste0(
paste0(
"", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
'"', x[i, ]$original_input, '"',
" -> ",
paste0(
"", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
'"', x[i, ]$original_input, '"',
" -> ",
paste0(
font_bold(italicise(x[i, ]$fullname)),
" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
)
),
collapse = "\n"
font_bold(italicise(x[i, ]$fullname)),
" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
)
),
ifelse(x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
paste0(
strrep(" ", nchar(x[i, ]$original_input) + 6),
ifelse(x[i, ]$keep_synonyms == FALSE,
# Add note if result was coerced to accepted taxonomic name
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
# Or add note if result is currently another taxonomic name
font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
)
),
""
),
candidates,
sep = "\n"
collapse = "\n"
)
txt <- gsub("[\n]+", "\n", txt)
# remove first and last break
txt <- gsub("(^[\n]|[\n]$)", "", txt)
txt <- paste0("\n", txt, "\n")
message_(out, as_note = FALSE)
if (x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")]) {
out2 <- paste0(
strrep(" ", nchar(x[i, ]$original_input) + 6),
ifelse(x[i, ]$keep_synonyms == FALSE,
# Add note if result was coerced to accepted taxonomic name
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
# Or add note if result is currently another taxonomic name
font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
)
)
message_(out2, as_note = FALSE)
}
other_matches <- paste0(
"Also matched: ",
vector_and(
paste0(
candidates_formatted,
font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
),
quotes = FALSE, sort = FALSE
)
)
message_(other_matches, as_note = FALSE)
}
cat(txt)
if (isTRUE(any_maxed_out)) {
cat(font_blue(word_wrap("\nOnly the first ", n, " other matches of each record are shown. Run `print(mo_uncertainties(), n = ...)` to view more entries, or save `mo_uncertainties()` to an object.")))
cat("\n")
message_("Only the first ", n, " other matches of each record are shown. Run {.help [`print(mo_uncertainties(), n = ...)`](AMR::mo_uncertainties)} to view more entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
}
if (isTRUE(more_than_50)) {
cat(font_blue(word_wrap("\nOnly the first 50 uncertainties are shown. Run `View(mo_uncertainties())` to view all entries, or save `mo_uncertainties()` to an object.")))
cat("\n")
message_("Only the first 50 uncertainties are shown. Run {.help [`View(mo_uncertainties())`](AMR::mo_uncertainties)} to view all entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
}
}
@@ -1032,7 +1030,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
#' @noRd
print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
if (NROW(x) == 0) {
cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n")))
message_("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
return(invisible(NULL))
}
@@ -1043,14 +1041,17 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
rows <- seq_len(min(NROW(x), n))
message_(
"The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":\n",
paste0(" ", AMR_env$bullet_icon, " ", font_italic(x$old[rows], collapse = NULL), x$ref_old[rows],
" -> ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
collapse = "\n"
),
ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run {.code print(mo_renamed(), n = ...)} to view more entries (might be slow), or save {.fun mo_renamed} to an object."), "")
)
message_("The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":")
old_format <- format(paste0(font_italic(x$old[rows], collapse = NULL), x$ref_old[rows])) # format() will set trailing spaces for textual alignment
old_format <- gsub(" ", "\u00a0", old_format, fixed = TRUE)
for (old_tax in rows) {
message_("\u00a0\u00a0", AMR_env$bullet_icon, " ", old_format[old_tax], " -> ", font_italic(x$new[old_tax]), x$ref_new[old_tax], as_note = FALSE)
}
if (NROW(x) > n) {
message_("\u00a0\u00a0Only the first ", n, " (out of ", NROW(x), ") are shown. Run {.code print(mo_renamed(), n = ...)} to view more entries (might be slow), or save {.fun mo_renamed} to an object.",
as_note = FALSE
)
}
}
# UNDOCUMENTED HELPER FUNCTIONS -------------------------------------------