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(v1.4.0.9008) like variations
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118
R/mo_property.R
118
R/mo_property.R
@ -9,7 +9,7 @@
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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@ -29,7 +29,7 @@
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#' @inheritSection lifecycle Stable lifecycle
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#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]
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#' @param property one of the column names of the [microorganisms] data set or `"shortname"`
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#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
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#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
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#' @param ... other parameters passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
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#' @param open browse the URL using [utils::browseURL()]
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#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010:
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@ -38,7 +38,7 @@
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#' - `mo_ref("Shimwellia blattae")` will return `"Priest et al., 2010"` (without a message)
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#'
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#' The short name - [mo_shortname()] - almost always returns the first character of the genus and the full species, like `"E. coli"`. Exceptions are abbreviations of staphylococci (like *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. In other words, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.
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#'
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#'
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#' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.
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#'
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#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [is_gram_negative()] and [is_gram_positive()] always return `TRUE` or `FALSE`, even for species outside the kingdom of Bacteria.
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@ -148,7 +148,7 @@
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mo_name <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
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}
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@ -161,20 +161,20 @@ mo_fullname <- mo_name
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mo_shortname <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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replace_empty <- function(x) {
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x[x == ""] <- "spp."
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x
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}
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# get first char of genus and complete species in English
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genera <- mo_genus(x.mo, language = NULL)
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shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
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# exceptions for where no species is known
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shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"]
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# exceptions for Staphylococci
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@ -184,7 +184,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
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# unknown species etc.
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shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
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load_mo_failures_uncertainties_renamed(metadata)
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translate_AMR(shortnames, language = language, only_unknown = FALSE)
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}
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@ -194,7 +194,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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mo_subspecies <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -203,7 +203,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
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mo_species <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -212,7 +212,7 @@ mo_species <- function(x, language = get_locale(), ...) {
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mo_genus <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -221,7 +221,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
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mo_family <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -230,7 +230,7 @@ mo_family <- function(x, language = get_locale(), ...) {
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mo_order <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -239,7 +239,7 @@ mo_order <- function(x, language = get_locale(), ...) {
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mo_class <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -248,7 +248,7 @@ mo_class <- function(x, language = get_locale(), ...) {
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mo_phylum <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -257,7 +257,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
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mo_kingdom <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -270,7 +270,7 @@ mo_domain <- mo_kingdom
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mo_type <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE)
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}
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@ -279,10 +279,10 @@ mo_type <- function(x, language = get_locale(), ...) {
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mo_gramstain <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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x.phylum <- mo_phylum(x.mo)
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# DETERMINE GRAM STAIN FOR BACTERIA
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# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
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@ -303,25 +303,35 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
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"Firmicutes",
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"Tenericutes")
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| x.mo == "B_GRAMP"] <- "Gram-positive"
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load_mo_failures_uncertainties_renamed(metadata)
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translate_AMR(x, language = language, only_unknown = FALSE)
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}
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#' @rdname mo_property
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#' @export
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is_gram_negative <- function(x, ...) {
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is_gram_negative <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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grams <- mo_gramstain(x, language = NULL, ...)
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"Gram-negative" == grams & !is.na(grams)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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grams <- mo_gramstain(x.mo, language = NULL)
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load_mo_failures_uncertainties_renamed(metadata)
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grams == "Gram-negative" & !is.na(grams)
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}
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#' @rdname mo_property
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#' @export
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is_gram_positive <- function(x, ...) {
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is_gram_positive <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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grams <- mo_gramstain(x, language = NULL, ...)
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"Gram-positive" == grams & !is.na(grams)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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grams <- mo_gramstain(x.mo, language = NULL)
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load_mo_failures_uncertainties_renamed(metadata)
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grams == "Gram-positive" & !is.na(grams)
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}
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#' @rdname mo_property
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@ -329,7 +339,7 @@ is_gram_positive <- function(x, ...) {
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mo_snomed <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "snomed", language = language, ...)
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}
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@ -338,7 +348,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
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mo_ref <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "ref", language = language, ...)
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}
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@ -347,7 +357,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
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mo_authors <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- mo_validate(x = x, property = "ref", language = language, ...)
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# remove last 4 digits and presumably the comma and space that preceed them
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x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
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@ -359,7 +369,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
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mo_year <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- mo_validate(x = x, property = "ref", language = language, ...)
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# get last 4 digits
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x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
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@ -371,7 +381,7 @@ mo_year <- function(x, language = get_locale(), ...) {
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mo_rank <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "rank", language = language, ...)
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}
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@ -380,10 +390,10 @@ mo_rank <- function(x, language = get_locale(), ...) {
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mo_taxonomy <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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result <- list(kingdom = mo_kingdom(x, language = language),
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phylum = mo_phylum(x, language = language),
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class = mo_class(x, language = language),
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@ -392,7 +402,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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genus = mo_genus(x, language = language),
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species = mo_species(x, language = language),
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subspecies = mo_subspecies(x, language = language))
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load_mo_failures_uncertainties_renamed(metadata)
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result
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}
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@ -402,10 +412,10 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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mo_synonyms <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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IDs <- mo_name(x = x, language = NULL)
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syns <- lapply(IDs, function(newname) {
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res <- sort(microorganisms.old[which(microorganisms.old$fullname_new == newname), "fullname"])
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@ -421,7 +431,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
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} else {
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result <- unlist(syns)
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}
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load_mo_failures_uncertainties_renamed(metadata)
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result
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}
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@ -431,10 +441,10 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
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mo_info <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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info <- lapply(x, function(y)
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c(mo_taxonomy(y, language = language),
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list(synonyms = mo_synonyms(y),
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@ -447,7 +457,7 @@ mo_info <- function(x, language = get_locale(), ...) {
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} else {
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result <- info[[1L]]
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}
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load_mo_failures_uncertainties_renamed(metadata)
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result
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}
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@ -458,11 +468,11 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(open, allow_class = "logical", has_length = 1)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo <- as.mo(x = x, language = language, ... = ...)
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mo_names <- mo_name(mo)
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metadata <- get_mo_failures_uncertainties_renamed()
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df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
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pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
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df$url <- ifelse(df$source == "CoL",
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@ -472,14 +482,14 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
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NA_character_))
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u <- df$url
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names(u) <- mo_names
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if (open == TRUE) {
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if (length(u) > 1) {
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warning("only the first URL will be opened, as `browseURL()` only suports one string.")
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}
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utils::browseURL(u[1L])
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}
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load_mo_failures_uncertainties_renamed(metadata)
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u
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}
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@ -491,18 +501,18 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
mo_validate <- function(x, property, language, ...) {
|
||||
check_dataset_integrity()
|
||||
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & length(list(...)) == 0, error = function(e) FALSE)) {
|
||||
# special case for mo_* functions where class is already <mo>
|
||||
return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
|
||||
}
|
||||
|
||||
|
||||
dots <- list(...)
|
||||
Becker <- dots$Becker
|
||||
if (is.null(Becker)) {
|
||||
@ -512,14 +522,14 @@ mo_validate <- function(x, property, language, ...) {
|
||||
if (is.null(Lancefield)) {
|
||||
Lancefield <- FALSE
|
||||
}
|
||||
|
||||
|
||||
# try to catch an error when inputting an invalid parameter
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
if (is.mo(x)
|
||||
& !Becker %in% c(TRUE, "all")
|
||||
|
||||
if (is.mo(x)
|
||||
& !Becker %in% c(TRUE, "all")
|
||||
& !Lancefield %in% c(TRUE, "all")) {
|
||||
# this will not reset mo_uncertainties and mo_failures
|
||||
# because it's already a valid MO
|
||||
@ -529,7 +539,7 @@ mo_validate <- function(x, property, language, ...) {
|
||||
| Lancefield %in% c(TRUE, "all")) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
}
|
||||
|
||||
|
||||
if (property == "mo") {
|
||||
return(to_class_mo(x))
|
||||
} else if (property == "snomed") {
|
||||
|
||||
Reference in New Issue
Block a user