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prepare for morphology

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dr. M.S. (Matthijs) Berends
2026-05-04 22:57:42 +02:00
parent a5e8beff69
commit cead31bed0
3 changed files with 148 additions and 3 deletions
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19
R/mo_property.R
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@@ -56,7 +56,7 @@
#'
#' Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) is based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials).
#'
#' Determination of bacterial oxygen tolerance ([mo_oxygen_tolerance()]) is 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.
#' Determination of both bacterial oxygen tolerance ([mo_oxygen_tolerance()]) and morphology ([mo_morphology()]) are based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria.
#'
#' 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`) is 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.
#'
@@ -462,8 +462,9 @@ mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = get
}
#' @rdname mo_property
#' @param add_morphology a [logical] to indicate whether the morphology (from [mo_morphology()]) should be added to the Gram stain result, e.g. `"Gram-negative rods"` instead of `"Gram-negative"`. The default is `FALSE`.
#' @export
mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), add_morphology = FALSE, ...) {
if (missing(x)) {
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_gramstain")
@@ -636,6 +637,20 @@ mo_is_anaerobic <- function(x, language = get_AMR_locale(), keep_synonyms = getO
out
}
#' @rdname mo_property
#' @export
mo_morphology <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_morphology")
}
meet_criteria(x, allow_NA = TRUE)
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
mo_validate(x = x, property = "morphology", language = language, keep_synonyms = keep_synonyms, ...)
}
#' @rdname mo_property
#' @export
mo_snomed <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {