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https://github.com/msberends/AMR.git
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(v0.7.1.9005) new rsi calculations, atc class removal
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@ -148,7 +148,9 @@ mo_fullname <- mo_name
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#' @importFrom dplyr %>% mutate pull
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#' @export
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mo_shortname <- function(x, language = get_locale(), ...) {
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x.mo <- as.mo(x, ...)
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x.mo <- AMR::as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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# get first char of genus and complete species in English
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shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", mo_species(x.mo, language = NULL))
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@ -158,6 +160,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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# exceptions for Streptococci
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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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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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@ -218,8 +221,10 @@ mo_type <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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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 = NULL)
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x.mo <- AMR::as.mo(x, ...)
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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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# It says this:
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@ -232,13 +237,15 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
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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 = NULL) == "Bacteria"] <- "Gram-negative"
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x[mo_kingdom(x.mo) == "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")
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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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@ -276,7 +283,9 @@ mo_rank <- function(x, ...) {
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#' @export
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mo_taxonomy <- function(x, language = get_locale(), ...) {
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x <- AMR::as.mo(x, ...)
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base::list(kingdom = AMR::mo_kingdom(x, language = language),
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metadata <- get_mo_failures_uncertainties_renamed()
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result <- base::list(kingdom = AMR::mo_kingdom(x, language = language),
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phylum = AMR::mo_phylum(x, language = language),
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class = AMR::mo_class(x, language = language),
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order = AMR::mo_order(x, language = language),
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@ -284,12 +293,17 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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genus = AMR::mo_genus(x, language = language),
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species = AMR::mo_species(x, language = language),
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subspecies = AMR::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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#' @rdname mo_property
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#' @export
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mo_synonyms <- function(x, ...) {
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x <- as.mo(x, ...)
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x <- AMR::as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL)
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syns <- lapply(IDs, function(col_id) {
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res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
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@ -301,16 +315,21 @@ mo_synonyms <- function(x, ...) {
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})
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if (length(syns) > 1) {
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names(syns) <- mo_fullname(x)
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syns
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result <- syns
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} else {
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unlist(syns)
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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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#' @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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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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@ -318,10 +337,13 @@ mo_info <- function(x, language = get_locale(), ...) {
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ref = mo_ref(y))))
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if (length(info) > 1) {
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names(info) <- mo_fullname(x)
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info
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result <- info
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} else {
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info[[1L]]
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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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#' @rdname mo_property
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@ -330,6 +352,8 @@ mo_info <- function(x, language = get_locale(), ...) {
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#' @export
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mo_url <- function(x, open = FALSE, ...) {
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mo <- AMR::as.mo(x = x, ... = ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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df <- data.frame(mo, stringsAsFactors = FALSE) %>%
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left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>%
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mutate(url = case_when(source == "CoL" ~
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@ -347,6 +371,8 @@ mo_url <- function(x, open = FALSE, ...) {
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}
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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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