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new species groups, updated clinical breakpoints
This commit is contained in:
295
R/mo.R
295
R/mo.R
@ -1,11 +1,11 @@
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# ==================================================================== #
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# TITLE #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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@ -169,7 +169,7 @@ as.mo <- function(x,
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meet_criteria(cleaning_regex, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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language <- validate_language(language)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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add_MO_lookup_to_AMR_env()
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if (tryCatch(all(x %in% c(AMR_env$MO_lookup$mo, NA)), error = function(e) FALSE) &&
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@ -180,28 +180,23 @@ as.mo <- function(x,
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# is.mo() won't work - MO codes might change between package versions
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return(set_clean_class(x, new_class = c("mo", "character")))
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}
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# start off with replaced language-specific non-ASCII characters with ASCII characters
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x <- parse_and_convert(x)
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# replace mo codes used in older package versions
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x <- replace_old_mo_codes(x, property = "mo")
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# ignore cases that match the ignore pattern
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x <- replace_ignore_pattern(x, ignore_pattern)
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x_lower <- tolower(x)
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complexes <- x[trimws2(x_lower) %like_case% " (complex|group)$"]
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if (length(complexes) > 0 && identical(cleaning_regex, mo_cleaning_regex()) && !any(AMR_env$MO_lookup$fullname[which(AMR_env$MO_lookup$source == "Added by user")] %like% "(group|complex)", na.rm = TRUE)) {
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warning_("in `as.mo()`: 'complex' and 'group' were ignored from the input in ", length(complexes), " case", ifelse(length(complexes) > 1, "s", ""), ", as they are currently not supported.\nYou can add your own microorganism with `add_custom_microorganisms()`.", call = FALSE)
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}
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# WHONET: xxx = no growth
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x[x_lower %in% c("", "xxx", "na", "nan")] <- NA_character_
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out <- rep(NA_character_, length(x))
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# below we use base R's match(), known for powering '%in%', and incredibly fast!
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# From reference_df ----
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reference_df <- repair_reference_df(reference_df)
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if (!is.null(reference_df)) {
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@ -233,33 +228,33 @@ as.mo <- function(x,
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" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this. This note will be shown once per session for this input."
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)
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}
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# For all other input ----
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if (any(is.na(out) & !is.na(x))) {
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# reset uncertainties
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AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, ]
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AMR_env$mo_failures <- NULL
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# Laboratory systems: remove (translated) entries like "no growth", "not E. coli", etc.
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x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
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x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") ")] <- NA_character_
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# groups are in our taxonomic table with a capital G
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x <- gsub(" group( |$)", " Group\\1", x, perl = TRUE)
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# run over all unique leftovers
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x_unique <- unique(x[is.na(out) & !is.na(x)])
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# set up progress bar
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progress <- progress_ticker(n = length(x_unique), n_min = 10, print = info)
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on.exit(close(progress))
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msg <- character(0)
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# run it
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x_coerced <- vapply(FUN.VALUE = character(1), x_unique, function(x_search) {
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progress$tick()
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# some required cleaning steps
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x_out <- trimws2(x_search)
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# this applies the `cleaning_regex` argument, which defaults to mo_cleaning_regex()
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@ -269,28 +264,28 @@ as.mo <- function(x,
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x_out <- tolower(x_out)
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# when x_search_cleaned are only capitals (such as in codes), make them lowercase to increase matching score
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x_search_cleaned[x_search_cleaned == toupper(x_search_cleaned)] <- x_out[x_search_cleaned == toupper(x_search_cleaned)]
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# first check if cleaning led to an exact result, case-insensitive
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if (x_out %in% AMR_env$MO_lookup$fullname_lower) {
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return(as.character(AMR_env$MO_lookup$mo[match(x_out, AMR_env$MO_lookup$fullname_lower)]))
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}
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# input must not be too short
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if (nchar(x_out) < 3) {
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return("UNKNOWN")
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}
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# take out the parts, split by space
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x_parts <- strsplit(gsub("-", " ", x_out, fixed = TRUE), " ", fixed = TRUE)[[1]]
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# do a pre-match on first character (and if it contains a space, first chars of first two terms)
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if (length(x_parts) %in% c(2, 3)) {
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# for genus + species + subspecies
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if (nchar(gsub("[^a-z]", "", x_parts[1], perl = TRUE)) <= 3) {
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filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) &
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(AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) |
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AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) |
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AMR_env$MO_lookup$subspecies_first == substr(x_parts[3], 1, 1)))
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AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) |
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AMR_env$MO_lookup$subspecies_first == substr(x_parts[3], 1, 1)))
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} else {
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filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) |
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AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) |
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@ -325,7 +320,7 @@ as.mo <- function(x,
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} else {
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mo_to_search <- AMR_env$MO_lookup$fullname[filtr]
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}
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AMR_env$mo_to_search <- mo_to_search
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# determine the matching score on the original search value
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m <- mo_matching_score(x = x_search_cleaned, n = mo_to_search)
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@ -347,7 +342,7 @@ as.mo <- function(x,
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m[m < minimum_matching_score] <- NA_real_
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minimum_matching_score_current <- minimum_matching_score
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}
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top_hits <- mo_to_search[order(m, decreasing = TRUE, na.last = NA)] # na.last = NA will remove the NAs
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if (length(top_hits) == 0) {
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warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), 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)
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@ -380,12 +375,12 @@ as.mo <- function(x,
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# the actual result:
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as.character(result_mo)
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})
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# remove progress bar from console
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close(progress)
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# expand from unique again
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out[is.na(out)] <- x_coerced[match(x[is.na(out)], x_unique)]
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# Throw note about uncertainties ----
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if (isTRUE(info) && NROW(AMR_env$mo_uncertainties) > 0) {
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if (message_not_thrown_before("as.mo", "uncertainties", AMR_env$mo_uncertainties$original_input)) {
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@ -408,14 +403,14 @@ as.mo <- function(x,
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"Microorganism translation was uncertain for ", examples,
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". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add custom entries."
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))
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for (m in msg) {
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message_(m)
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}
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}
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}
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} # end of loop over all yet unknowns
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# Keep or replace synonyms ----
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lpsn_matches <- AMR_env$MO_lookup$lpsn_renamed_to[match(out, AMR_env$MO_lookup$mo)]
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lpsn_matches[!lpsn_matches %in% AMR_env$MO_lookup$lpsn] <- NA
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@ -438,14 +433,14 @@ as.mo <- function(x,
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# keep synonyms is TRUE, so check if any do have synonyms
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warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " old taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
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}
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# Apply Becker ----
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if (isTRUE(Becker) || Becker == "all") {
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# warn when species found that are not in:
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# - Becker et al. 2014, PMID 25278577
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# - Becker et al. 2019, PMID 30872103
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# - Becker et al. 2020, PMID 32056452
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# comment below code if all staphylococcal species are categorised as CoNS/CoPS
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post_Becker <- paste(
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"Staphylococcus",
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@ -454,13 +449,13 @@ as.mo <- function(x,
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if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
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if (message_not_thrown_before("as.mo", "becker")) {
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warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
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vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
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". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
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immediate = TRUE, call = FALSE
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vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
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". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
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immediate = TRUE, call = FALSE
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)
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}
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}
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# 'MO_CONS' and 'MO_COPS' are 'mo' vectors created in R/_pre_commit_hook.R
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out[out %in% MO_CONS] <- "B_STPHY_CONS"
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out[out %in% MO_COPS] <- "B_STPHY_COPS"
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@ -468,11 +463,11 @@ as.mo <- function(x,
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out[out == "B_STPHY_AURS"] <- "B_STPHY_COPS"
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}
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}
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# Apply Lancefield ----
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if (isTRUE(Lancefield) || Lancefield == "all") {
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# (using `%like_case%` to also match subspecies)
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# group A - S. pyogenes
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out[out %like_case% "^B_STRPT_PYGN(_|$)"] <- "B_STRPT_GRPA"
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# group B - S. agalactiae
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@ -493,17 +488,17 @@ as.mo <- function(x,
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out[out %like_case% "^B_STRPT_SLVR(_|$)"] <- "B_STRPT_GRPK"
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# group L - only S. dysgalactiae which is also group C & G, so ignore it here
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}
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# All unknowns ----
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out[is.na(out) & !is.na(x)] <- "UNKNOWN"
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AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !x %in% c("UNKNOWN", "con") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
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AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !toupper(x) %in% c("UNKNOWN", "CON", "UNK") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
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if (length(AMR_env$mo_failures) > 0) {
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warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.", call = FALSE)
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}
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# Return class ----
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set_clean_class(out,
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new_class = c("mo", "character")
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new_class = c("mo", "character")
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)
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}
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@ -526,13 +521,13 @@ mo_uncertainties <- function() {
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mo_renamed <- function() {
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add_MO_lookup_to_AMR_env()
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x <- AMR_env$mo_renamed
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x$new <- synonym_mo_to_accepted_mo(x$old)
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mo_old <- AMR_env$MO_lookup$fullname[match(x$old, AMR_env$MO_lookup$mo)]
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mo_new <- AMR_env$MO_lookup$fullname[match(x$new, AMR_env$MO_lookup$mo)]
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ref_old <- AMR_env$MO_lookup$ref[match(x$old, AMR_env$MO_lookup$mo)]
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ref_new <- AMR_env$MO_lookup$ref[match(x$new, AMR_env$MO_lookup$mo)]
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df_renamed <- data.frame(
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old = mo_old,
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new = mo_new,
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@ -572,7 +567,7 @@ mo_cleaning_regex <- function() {
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"|",
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"([({]|\\[).+([})]|\\])",
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"|",
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"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|var|serogr.?up|e?species)[.]*( |$|(complex|group)$))"
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"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|var|serogr.?up|e?species|titer|dummy)[.]*|( Ig[ADEGM])( |$))"
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)
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}
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@ -586,30 +581,30 @@ pillar_shaft.mo <- function(x, ...) {
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out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
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# and grey out every _
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out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
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# markup NA and UNKNOWN
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out[is.na(x)] <- font_na(" NA")
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out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
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# markup manual codes
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out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo] <- font_blue(out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo], collapse = NULL)
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df <- tryCatch(get_current_data(arg_name = "x", call = 0),
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error = function(e) NULL
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error = function(e) NULL
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)
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if (!is.null(df)) {
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mo_cols <- vapply(FUN.VALUE = logical(1), df, is.mo)
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} else {
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mo_cols <- NULL
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}
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all_mos <- c(AMR_env$MO_lookup$mo, NA)
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if (!all(x %in% all_mos) ||
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(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) {
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(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) {
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# markup old mo codes
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out[!x %in% all_mos] <- font_italic(
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font_na(x[!x %in% all_mos],
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collapse = NULL
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collapse = NULL
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),
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collapse = NULL
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)
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@ -625,15 +620,15 @@ pillar_shaft.mo <- function(x, ...) {
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call = FALSE
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)
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}
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# make it always fit exactly
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max_char <- max(nchar(x))
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if (is.na(max_char)) {
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max_char <- 12
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}
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create_pillar_column(out,
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align = "left",
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width = max_char + ifelse(any(x %in% c(NA, "UNKNOWN")), 2, 0)
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align = "left",
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width = max_char + ifelse(any(x %in% c(NA, "UNKNOWN")), 2, 0)
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)
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}
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@ -656,21 +651,21 @@ freq.mo <- function(x, ...) {
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.add_header = list(
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`Gram-negative` = paste0(
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format(sum(grams == "Gram-negative", na.rm = TRUE),
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big.mark = " ",
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decimal.mark = "."
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big.mark = " ",
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decimal.mark = "."
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),
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" (", percentage(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams),
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digits = digits
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digits = digits
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),
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")"
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),
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`Gram-positive` = paste0(
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format(sum(grams == "Gram-positive", na.rm = TRUE),
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big.mark = " ",
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decimal.mark = "."
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big.mark = " ",
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decimal.mark = "."
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),
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" (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams),
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digits = digits
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digits = digits
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),
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")"
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),
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@ -832,26 +827,26 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
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more_than_50 <- TRUE
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x <- x[1:50, , drop = FALSE]
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}
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cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
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add_MO_lookup_to_AMR_env()
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col_red <- function(x) font_rose_bg(font_black(x, collapse = NULL), collapse = NULL)
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||||
col_orange <- function(x) font_orange_bg(font_black(x, collapse = NULL), collapse = NULL)
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||||
col_yellow <- function(x) font_yellow_bg(font_black(x, collapse = NULL), collapse = NULL)
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||||
col_green <- function(x) font_green_bg(font_black(x, collapse = NULL), collapse = NULL)
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||||
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||||
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col_red <- function(x) font_rose_bg(font_black(x, collapse = NULL, adapt = FALSE), collapse = NULL)
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||||
col_orange <- function(x) font_orange_bg(font_black(x, collapse = NULL, adapt = FALSE), collapse = NULL)
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||||
col_yellow <- function(x) font_yellow_bg(font_black(x, collapse = NULL, adapt = FALSE), collapse = NULL)
|
||||
col_green <- function(x) font_green_bg(font_black(x, collapse = NULL, adapt = FALSE), collapse = NULL)
|
||||
|
||||
if (has_colour()) {
|
||||
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"),
|
||||
add_fn = font_blue
|
||||
col_red(" 0.000-0.549 "),
|
||||
col_orange(" 0.550-0.649 "),
|
||||
col_yellow(" 0.650-0.749 "),
|
||||
col_green(" 0.750-1.000"),
|
||||
add_fn = font_blue
|
||||
), font_green_bg(" "), "\n", sep = "")
|
||||
}
|
||||
|
||||
|
||||
score_set_colour <- function(text, scores) {
|
||||
# set colours to scores
|
||||
text[scores >= 0.75] <- col_green(text[scores >= 0.75])
|
||||
@ -860,7 +855,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
|
||||
text[scores < 0.55] <- col_red(text[scores < 0.55])
|
||||
text
|
||||
}
|
||||
|
||||
|
||||
txt <- ""
|
||||
any_maxed_out <- FALSE
|
||||
for (i in seq_len(nrow(x))) {
|
||||
@ -872,15 +867,15 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
|
||||
}
|
||||
scores <- mo_matching_score(x = x[i, ]$input, n = candidates)
|
||||
n_candidates <- length(candidates)
|
||||
|
||||
|
||||
candidates_formatted <- italicise(candidates)
|
||||
scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
|
||||
scores_formatted <- score_set_colour(scores_formatted, scores)
|
||||
|
||||
|
||||
# sort on descending scores
|
||||
candidates_formatted <- candidates_formatted[order(1 - scores)]
|
||||
scores_formatted <- scores_formatted[order(1 - scores)]
|
||||
|
||||
|
||||
candidates <- word_wrap(
|
||||
paste0(
|
||||
"Also matched: ",
|
||||
@ -898,42 +893,42 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
|
||||
} else {
|
||||
candidates <- ""
|
||||
}
|
||||
|
||||
|
||||
score <- mo_matching_score(
|
||||
x = x[i, ]$input,
|
||||
n = x[i, ]$fullname
|
||||
)
|
||||
score_formatted <- trimws(formatC(round(score, 3), format = "f", digits = 3))
|
||||
txt <- paste(txt,
|
||||
paste0(
|
||||
paste0(
|
||||
"", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
|
||||
'"', x[i, ]$original_input, '"',
|
||||
" -> ",
|
||||
paste0(
|
||||
font_bold(italicise(x[i, ]$fullname)),
|
||||
" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
|
||||
)
|
||||
),
|
||||
collapse = "\n"
|
||||
),
|
||||
# Add note if result was coerced to accepted taxonomic name
|
||||
ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
|
||||
paste0(
|
||||
strrep(" ", nchar(x[i, ]$original_input) + 6),
|
||||
font_red(paste0("This old taxonomic name was converted to ", font_italic(AMR_env$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, ]$mo), ")."), collapse = NULL)
|
||||
),
|
||||
""
|
||||
),
|
||||
candidates,
|
||||
sep = "\n"
|
||||
paste0(
|
||||
paste0(
|
||||
"", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
|
||||
'"', x[i, ]$original_input, '"',
|
||||
" -> ",
|
||||
paste0(
|
||||
font_bold(italicise(x[i, ]$fullname)),
|
||||
" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
|
||||
)
|
||||
),
|
||||
collapse = "\n"
|
||||
),
|
||||
# Add note if result was coerced to accepted taxonomic name
|
||||
ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
|
||||
paste0(
|
||||
strrep(" ", nchar(x[i, ]$original_input) + 6),
|
||||
font_red(paste0("This old taxonomic name was converted to ", font_italic(AMR_env$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, ]$mo), ")."), collapse = NULL)
|
||||
),
|
||||
""
|
||||
),
|
||||
candidates,
|
||||
sep = "\n"
|
||||
)
|
||||
txt <- gsub("[\n]+", "\n", txt)
|
||||
# remove first and last break
|
||||
txt <- gsub("(^[\n]|[\n]$)", "", txt)
|
||||
txt <- paste0("\n", txt, "\n")
|
||||
}
|
||||
|
||||
|
||||
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.")))
|
||||
@ -951,19 +946,19 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
|
||||
cat(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of `as.mo()` or any `mo_*()` function are stored.\n", add_fn = font_blue))
|
||||
return(invisible(NULL))
|
||||
}
|
||||
|
||||
|
||||
x$ref_old[!is.na(x$ref_old)] <- paste0(" (", gsub("et al.", font_italic("et al."), x$ref_old[!is.na(x$ref_old)], fixed = TRUE), ")")
|
||||
x$ref_new[!is.na(x$ref_new)] <- paste0(" (", gsub("et al.", font_italic("et al."), x$ref_new[!is.na(x$ref_new)], fixed = TRUE), ")")
|
||||
x$ref_old[is.na(x$ref_old)] <- " (author unknown)"
|
||||
x$ref_new[is.na(x$ref_new)] <- " (author unknown)"
|
||||
|
||||
|
||||
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$ref_new[rows],
|
||||
collapse = "\n"
|
||||
" -> ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
|
||||
collapse = "\n"
|
||||
),
|
||||
ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run `print(mo_renamed(), n = ...)` to view more entries (might be slow), or save `mo_renamed()` to an object."), "")
|
||||
)
|
||||
@ -975,51 +970,51 @@ convert_colloquial_input <- function(x) {
|
||||
x.bak <- trimws2(x)
|
||||
x <- trimws2(tolower(x))
|
||||
out <- rep(NA_character_, length(x))
|
||||
|
||||
|
||||
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
|
||||
out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "^g[abcdefghijkl]s$"],
|
||||
perl = TRUE
|
||||
out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "^g[abcdefghijkl]s$"],
|
||||
perl = TRUE
|
||||
)
|
||||
# Streptococci in different languages, like "estreptococos grupo B"
|
||||
out[x %like_case% "strepto[ck]o[ck].* [abcdefghijkl]$"] <- gsub(".*e?strepto[ck]o[ck].* ([abcdefghijkl])$",
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "strepto[ck]o[ck].* [abcdefghijkl]$"],
|
||||
perl = TRUE
|
||||
out[x %like_case% "strepto[ck]o[ck][a-zA-Z]* [abcdefghijkl]$"] <- gsub(".*e?strepto[ck]o[ck].* ([abcdefghijkl])$",
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "strepto[ck]o[ck][a-zA-Z]* [abcdefghijkl]$"],
|
||||
perl = TRUE
|
||||
)
|
||||
out[x %like_case% "strep[a-z]* group [abcdefghijkl]$"] <- gsub(".* ([abcdefghijkl])$",
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "strep[a-z]* group [abcdefghijkl]$"],
|
||||
perl = TRUE
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "strep[a-z]* group [abcdefghijkl]$"],
|
||||
perl = TRUE
|
||||
)
|
||||
out[x %like_case% "group [abcdefghijkl] strepto[ck]o[ck]"] <- gsub(".*group ([abcdefghijkl]) strepto[ck]o[ck].*",
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "group [abcdefghijkl] strepto[ck]o[ck]"],
|
||||
perl = TRUE
|
||||
"B_STRPT_GRP\\U\\1",
|
||||
x[x %like_case% "group [abcdefghijkl] strepto[ck]o[ck]"],
|
||||
perl = TRUE
|
||||
)
|
||||
out[x %like_case% "ha?emoly.*strep"] <- "B_STRPT_HAEM"
|
||||
out[x %like_case% "(strepto.* mil+er+i|^mgs[^a-z]*$)"] <- "B_STRPT_MILL"
|
||||
out[x %like_case% "mil+er+i gr"] <- "B_STRPT_MILL"
|
||||
out[x %like_case% "((strepto|^s).* viridans|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
|
||||
out[x %like_case% "(viridans.* (strepto|^s).*|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
|
||||
|
||||
|
||||
# Salmonella in different languages, like "Salmonella grupo B"
|
||||
out[x %like_case% "salmonella.* [abcdefgh]$"] <- gsub(".*salmonella.* ([abcdefgh])$",
|
||||
"B_SLMNL_GRP\\U\\1",
|
||||
x[x %like_case% "salmonella.* [abcdefgh]$"],
|
||||
perl = TRUE
|
||||
"B_SLMNL_GRP\\U\\1",
|
||||
x[x %like_case% "salmonella.* [abcdefgh]$"],
|
||||
perl = TRUE
|
||||
)
|
||||
out[x %like_case% "group [abcdefgh] salmonella"] <- gsub(".*group ([abcdefgh]) salmonella*",
|
||||
"B_SLMNL_GRP\\U\\1",
|
||||
x[x %like_case% "group [abcdefgh] salmonella"],
|
||||
perl = TRUE
|
||||
"B_SLMNL_GRP\\U\\1",
|
||||
x[x %like_case% "group [abcdefgh] salmonella"],
|
||||
perl = TRUE
|
||||
)
|
||||
|
||||
|
||||
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese)
|
||||
out[x %like_case% "([ck]oagulas[ea].negatie?[vf]|^[ck]o?ns[^a-z]*$)"] <- "B_STPHY_CONS"
|
||||
out[x %like_case% "([ck]oagulas[ea].positie?[vf]|^[ck]o?ps[^a-z]*$)"] <- "B_STPHY_COPS"
|
||||
|
||||
|
||||
# Gram stains
|
||||
out[x %like_case% "gram[ -]?neg.*"] <- "B_GRAMN"
|
||||
out[x %like_case% "( |^)gram[-]( |$)"] <- "B_GRAMN"
|
||||
@ -1032,19 +1027,19 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
|
||||
# yeasts and fungi
|
||||
out[x %like_case% "^yeast?"] <- "F_YEAST"
|
||||
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
|
||||
|
||||
|
||||
# trivial names known to the field
|
||||
out[x %like_case% "meningo[ck]o[ck]"] <- "B_NESSR_MNNG"
|
||||
out[x %like_case% "gono[ck]o[ck]"] <- "B_NESSR_GNRR"
|
||||
out[x %like_case% "pneumo[ck]o[ck]"] <- "B_STRPT_PNMN"
|
||||
|
||||
|
||||
# unexisting names (con is the WHONET code for contamination)
|
||||
out[x %in% c("con", "other", "none", "unknown") | x %like_case% "virus"] <- "UNKNOWN"
|
||||
|
||||
|
||||
# WHONET has a lot of E. coli and Vibrio cholerae names
|
||||
out[x %like_case% "escherichia coli"] <- "B_ESCHR_COLI"
|
||||
out[x %like_case% "vibrio cholerae"] <- "B_VIBRI_CHLR"
|
||||
|
||||
|
||||
out
|
||||
}
|
||||
|
||||
@ -1136,7 +1131,7 @@ replace_old_mo_codes <- function(x, property) {
|
||||
name <- gsub(" .*", " ", name, fixed = TRUE)
|
||||
name <- paste0("^", name)
|
||||
results <- AMR_env$MO_lookup$mo[AMR_env$MO_lookup$kingdom %like_case% kingdom &
|
||||
AMR_env$MO_lookup$fullname_lower %like_case% name]
|
||||
AMR_env$MO_lookup$fullname_lower %like_case% name]
|
||||
if (length(results) > 1) {
|
||||
all_direct_matches <<- FALSE
|
||||
}
|
||||
@ -1173,8 +1168,8 @@ replace_old_mo_codes <- function(x, property) {
|
||||
"to ", ifelse(n_solved == 1, "a ", ""),
|
||||
"currently used MO code", ifelse(n_solved == 1, "", "s"),
|
||||
ifelse(n_unsolved > 0,
|
||||
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
|
||||
"."
|
||||
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
|
||||
"."
|
||||
)
|
||||
)
|
||||
}
|
||||
@ -1203,19 +1198,19 @@ repair_reference_df <- function(reference_df) {
|
||||
# has valid own reference_df
|
||||
reference_df <- reference_df %pm>%
|
||||
pm_filter(!is.na(mo))
|
||||
|
||||
|
||||
# keep only first two columns, second must be mo
|
||||
if (colnames(reference_df)[1] == "mo") {
|
||||
reference_df <- reference_df %pm>% pm_select(2, "mo")
|
||||
} else {
|
||||
reference_df <- reference_df %pm>% pm_select(1, "mo")
|
||||
}
|
||||
|
||||
|
||||
# remove factors, just keep characters
|
||||
colnames(reference_df)[1] <- "x"
|
||||
reference_df[, "x"] <- as.character(reference_df[, "x", drop = TRUE])
|
||||
reference_df[, "mo"] <- as.character(reference_df[, "mo", drop = TRUE])
|
||||
|
||||
|
||||
# some MO codes might be old
|
||||
reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE], reference_df = NULL)
|
||||
reference_df
|
||||
@ -1237,10 +1232,10 @@ synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) {
|
||||
x_lpsn <- AMR_env$MO_lookup$lpsn_renamed_to[match(x, AMR_env$MO_lookup$mo)]
|
||||
x_gbif[!x_gbif %in% AMR_env$MO_lookup$gbif] <- NA
|
||||
x_lpsn[!x_lpsn %in% AMR_env$MO_lookup$lpsn] <- NA
|
||||
|
||||
|
||||
out <- ifelse(is.na(x_lpsn),
|
||||
AMR_env$MO_lookup$mo[match(x_gbif, AMR_env$MO_lookup$gbif)],
|
||||
AMR_env$MO_lookup$mo[match(x_lpsn, AMR_env$MO_lookup$lpsn)]
|
||||
AMR_env$MO_lookup$mo[match(x_gbif, AMR_env$MO_lookup$gbif)],
|
||||
AMR_env$MO_lookup$mo[match(x_lpsn, AMR_env$MO_lookup$lpsn)]
|
||||
)
|
||||
if (isTRUE(fill_in_accepted)) {
|
||||
x_accepted <- which(AMR_env$MO_lookup$status[match(x, AMR_env$MO_lookup$mo)] == "accepted")
|
||||
|
||||
Reference in New Issue
Block a user