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(v0.7.0.9005) ab algorithm update
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@ -69,8 +69,8 @@
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#' mo_shortname("E. coli") # "E. coli"
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#'
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#' ## other properties
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#' mo_gramstain("E. coli") # "Gram negative"
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#' mo_type("E. coli") # "Bacteria" (equal to kingdom)
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#' mo_gramstain("E. coli") # "Gram-negative"
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#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
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#' mo_rank("E. coli") # "species"
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#' mo_url("E. coli") # get the direct url to the online database entry
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#'
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@ -84,7 +84,7 @@
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#' mo_genus("MRSA") # "Staphylococcus"
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#' mo_species("MRSA") # "aureus"
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#' mo_shortname("MRSA") # "S. aureus"
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#' mo_gramstain("MRSA") # "Gram positive"
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#' mo_gramstain("MRSA") # "Gram-positive"
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#'
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#' mo_genus("VISA") # "Staphylococcus"
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#' mo_species("VISA") # "aureus"
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@ -133,15 +133,15 @@
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#'
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' mo_taxonomy("E. coli")
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#' # get a list with the taxonomy, the authors and the URL to the online database
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#' mo_info("E. coli")
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mo_name <- function(x, language = get_locale(), ...) {
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mo_fullname(x = x, language = language, ... = ...)
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translate_AMR(mo_validate(x = x, property = "fullname", ...), 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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mo_fullname <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "fullname", ...), language = language)
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}
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mo_fullname <- mo_name
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#' @rdname mo_property
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#' @importFrom dplyr %>% mutate pull
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@ -184,70 +184,61 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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res1[res1 != res2] <- res2_fullname
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result <- as.character(res1)
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t(result, language = language)
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translate_AMR(result, 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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mo_subspecies <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "subspecies", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "subspecies", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_species <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "species", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "species", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_genus <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "genus", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "genus", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_family <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "family", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "family", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_order <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "order", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "order", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_class <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "class", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "class", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_phylum <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "phylum", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "phylum", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_kingdom <- function(x, language = get_locale(), ...) {
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if (all(x %in% AMR::microorganisms$kingdom)) {
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return(x)
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}
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x <- as.mo(x, ...)
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kngdm <- mo_validate(x = x, property = "kingdom", ...)
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if (language != "en") {
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# translate only unknown, so "Bacteria" (the official taxonomic name) would not change
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kngdm[identical(x, "UNKNOWN")] <- t(kngdm[identical(x, "UNKNOWN")], language = language)
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}
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kngdm
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translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = TRUE)
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}
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#' @rdname mo_property
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#' @export
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mo_type <- function(x, language = get_locale(), ...) {
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t(mo_validate(x = x, property = "kingdom", ...), language = language)
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translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = FALSE)
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}
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#' @rdname mo_property
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@ -255,16 +246,26 @@ mo_type <- function(x, language = get_locale(), ...) {
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mo_gramstain <- function(x, language = get_locale(), ...) {
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x.mo <- as.mo(x, ...)
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x.phylum <- mo_phylum(x.mo, language = "en")
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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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# It says this:
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# Kingdom Bacteria (Cavalier-Smith, 2002)
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# Subkingdom Posibacteria (Cavalier-Smith, 2002)
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# Direct Children:
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# Phylum Actinobacteria (Cavalier-Smith, 2002)
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# Phylum Chloroflexi (Garrity and Holt, 2002)
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# Phylum Firmicutes (corrig. Gibbons and Murray, 1978)
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# Phylum Tenericutes (Murray, 1984)
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x <- NA_character_
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# make all bacteria Gram negative
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x[mo_kingdom(x.mo, language = "en") == "Bacteria"] <- "Gram-negative"
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# overwrite these phyla with Gram positive
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x[x.phylum %in% c("Actinobacteria",
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"Chloroflexi",
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"Firmicutes",
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"Tenericutes")] <- "Gram positive"
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x[x != "Gram positive"] <- "Gram negative"
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x[mo_kingdom(x.mo, language = "en") != "Bacteria"] <- NA_character_
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x[x.mo == "B_GRAMP"] <- "Gram positive"
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x[x.mo == "B_GRAMN"] <- "Gram negative"
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t(x, language = language)
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"Tenericutes")
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| x.mo == "B_GRAMP"] <- "Gram-positive"
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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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@ -311,6 +312,15 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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subspecies = mo_subspecies(x, language = language))
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}
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#' @rdname mo_property
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#' @export
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mo_info <- function(x, language = get_locale(), ...) {
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x <- AMR::as.mo(x, ...)
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c(mo_taxonomy(x, language = language),
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list(url = unname(mo_url(x, open = FALSE)),
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ref = mo_ref(x)))
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}
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#' @rdname mo_property
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#' @importFrom utils browseURL
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#' @importFrom dplyr %>% left_join select mutate case_when
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@ -349,7 +359,7 @@ mo_property <- function(x, property = 'fullname', language = get_locale(), ...)
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stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
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}
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t(mo_validate(x = x, property = property, ...), language = language)
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translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
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}
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mo_validate <- function(x, property, ...) {
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