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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47

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dr. M.S. (Matthijs) Berends
2021-08-16 21:54:34 +02:00
parent 4e1efd902c
commit a2d249962f
248 changed files with 2377 additions and 12201 deletions
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31
R/mo_property.R
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@ -42,7 +42,7 @@
#'
#' 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.
#'
#' 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 [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
#' 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, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
#'
#' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
#'
@ -364,25 +364,18 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
x.mo <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
x.phylum <- mo_phylum(x.mo)
# DETERMINE GRAM STAIN FOR BACTERIA
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
# It says this:
# Kingdom Bacteria (Cavalier-Smith, 2002)
# Subkingdom Posibacteria (Cavalier-Smith, 2002)
# Direct Children:
# Phylum Actinobacteria (Cavalier-Smith, 2002)
# Phylum Chloroflexi (Garrity and Holt, 2002)
# Phylum Firmicutes (corrig. Gibbons and Murray, 1978)
# Phylum Tenericutes (Murray, 1984)
x <- NA_character_
x <- rep(NA_character_, length(x))
# make all bacteria Gram negative
x[mo_kingdom(x.mo) == "Bacteria"] <- "Gram-negative"
# overwrite these phyla with Gram positive
x[x.phylum %in% c("Actinobacteria",
"Chloroflexi",
"Firmicutes",
"Tenericutes")
# overwrite these 4 phyla with Gram-positives
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002)
x[(mo_phylum(x.mo) %in% c("Actinobacteria",
"Chloroflexi",
"Firmicutes",
"Tenericutes") &
# but class Negativicutes (of phylum Firmicutes) are Gram-negative!
mo_class(x.mo) != "Negativicutes")
# and of course our own ID for Gram-positives
| x.mo == "B_GRAMP"] <- "Gram-positive"
load_mo_failures_uncertainties_renamed(metadata)
@ -477,7 +470,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
}
# show used version number once per session (pkg_env will reload every session)
if (message_not_thrown_before("intrinsic_resistant_version", entire_session = TRUE)) {
if (message_not_thrown_before("intrinsic_resistant_version.mo", entire_session = TRUE)) {
message_("Determining intrinsic resistance based on ",
format_eucast_version_nr(3.2, markdown = FALSE), ". ",
font_red("This note will be shown once per session."))