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(v2.1.1.9163) cleanup
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@ -53,7 +53,7 @@
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#' Determination of yeasts ([mo_is_yeast()]) will be based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).
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#'
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#' Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antibiotics).
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#'
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#'
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#' Determination of bacterial oxygen tolerance ([mo_oxygen_tolerance()]) will be based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria.
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#'
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#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) will be used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise.
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@ -107,12 +107,14 @@
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#' mo_rank("Klebsiella pneumoniae")
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#' mo_url("Klebsiella pneumoniae")
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#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
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#'
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#' mo_group_members(c("Streptococcus group A",
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#' "Streptococcus group C",
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#' "Streptococcus group G",
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#' "Streptococcus group L"))
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#'
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#'
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#' mo_group_members(c(
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#' "Streptococcus group A",
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#' "Streptococcus group C",
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#' "Streptococcus group G",
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#' "Streptococcus group L"
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#' ))
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#'
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#'
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#' # scientific reference -----------------------------------------------------
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#'
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@ -125,7 +127,7 @@
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#' mo_mycobank("Candida albicans")
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#' mo_mycobank("Candida krusei")
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#' mo_mycobank("Candida krusei", keep_synonyms = TRUE)
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#'
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#'
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#'
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#' # abbreviations known in the field -----------------------------------------
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#'
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@ -442,13 +444,16 @@ mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = get
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kngd <- AMR_env$MO_lookup$kingdom[match(x.mo, AMR_env$MO_lookup$mo)]
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rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)]
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out <- factor(case_when_AMR(prev <= 1.15 & kngd == "Bacteria" & rank != "genus" ~ "Pathogenic",
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prev < 2 & kngd == "Fungi" ~ "Potentially pathogenic",
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prev == 2 & kngd == "Bacteria" ~ "Non-pathogenic",
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kngd == "Bacteria" ~ "Potentially pathogenic",
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TRUE ~ "Unknown"),
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levels = c("Pathogenic", "Potentially pathogenic", "Non-pathogenic", "Unknown"),
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ordered = TRUE
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out <- factor(
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case_when_AMR(
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prev <= 1.15 & kngd == "Bacteria" & rank != "genus" ~ "Pathogenic",
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prev < 2 & kngd == "Fungi" ~ "Potentially pathogenic",
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prev == 2 & kngd == "Bacteria" ~ "Non-pathogenic",
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kngd == "Bacteria" ~ "Potentially pathogenic",
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TRUE ~ "Unknown"
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),
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levels = c("Pathogenic", "Potentially pathogenic", "Non-pathogenic", "Unknown"),
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ordered = TRUE
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)
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load_mo_uncertainties(metadata)
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@ -606,7 +611,7 @@ mo_oxygen_tolerance <- function(x, language = get_AMR_locale(), keep_synonyms =
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meet_criteria(x, allow_NA = TRUE)
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language <- validate_language(language)
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meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
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mo_validate(x = x, property = "oxygen_tolerance", language = language, keep_synonyms = keep_synonyms, ...)
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}
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@ -620,7 +625,7 @@ mo_is_anaerobic <- function(x, language = get_AMR_locale(), keep_synonyms = getO
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meet_criteria(x, allow_NA = TRUE)
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language <- validate_language(language)
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meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
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x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
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metadata <- get_mo_uncertainties()
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oxygen <- mo_oxygen_tolerance(x.mo, language = NULL, keep_synonyms = keep_synonyms)
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@ -716,7 +721,7 @@ mo_mycobank <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
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meet_criteria(x, allow_NA = TRUE)
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language <- validate_language(language)
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meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
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mo_validate(x = x, property = "mycobank", language = language, keep_synonyms = keep_synonyms, ...)
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}
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@ -836,21 +841,21 @@ mo_group_members <- function(x, language = get_AMR_locale(), keep_synonyms = get
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meet_criteria(x, allow_NA = TRUE)
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language <- validate_language(language)
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meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
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add_MO_lookup_to_AMR_env()
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x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
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metadata <- get_mo_uncertainties()
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members <- lapply(x.mo, function(y) {
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AMR::microorganisms.groups$mo_name[which(AMR::microorganisms.groups$mo_group == y)]
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})
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names(members) <- mo_name(x, keep_synonyms = TRUE, language = language)
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if (length(members) == 1) {
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members <- unname(unlist(members))
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}
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load_mo_uncertainties(metadata)
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members
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}
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@ -872,8 +877,10 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
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info <- lapply(x, function(y) {
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c(
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list(mo = as.character(y),
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rank = mo_rank(y, language = language, keep_synonyms = keep_synonyms)),
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list(
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mo = as.character(y),
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rank = mo_rank(y, language = language, keep_synonyms = keep_synonyms)
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),
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mo_taxonomy(y, language = language, keep_synonyms = keep_synonyms),
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list(
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status = mo_status(y, language = language, keep_synonyms = keep_synonyms),
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@ -920,7 +927,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
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x.rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)]
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x.name <- AMR_env$MO_lookup$fullname[match(x.mo, AMR_env$MO_lookup$mo)]
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x.lpsn <- AMR_env$MO_lookup$lpsn[match(x.mo, AMR_env$MO_lookup$mo)]
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x.mycobank <- AMR_env$MO_lookup$mycobank[match(x.mo, AMR_env$MO_lookup$mo)]
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x.gbif <- AMR_env$MO_lookup$gbif[match(x.mo, AMR_env$MO_lookup$mo)]
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@ -980,7 +987,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
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Lancefield <- FALSE
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}
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has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") || Lancefield %in% c(TRUE, "all")
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if (isFALSE(has_Becker_or_Lancefield) && isTRUE(keep_synonyms) && all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
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# fastest way to get properties
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if (property == "snomed") {
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@ -988,11 +995,10 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
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} else {
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x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
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}
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} else {
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# get microorganisms data set, but remove synonyms if keep_synonyms is FALSE
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mo_data_check <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE]
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if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) {
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# do nothing, just don't run the other if-else's
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} else if (all(x %in% c(unlist(mo_data_check[[property]]), NA)) && !has_Becker_or_Lancefield) {
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@ -1003,7 +1009,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
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x <- replace_old_mo_codes(x, property = property)
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x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
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}
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# get property reeaaally fast using match()
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if (property == "snomed") {
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x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)]))
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