mo_glims: Microorganisms Code from GLIMS10

In certe-medical-epidemiology/certetoolbox: A Certe R Package for Miscellaneous Functions

Microorganisms Code from GLIMS10

Description

This function is analogous to all ⁠mo_*⁠ functions of the AMR package, see AMR::mo_property().

Usage

mo_glims(
  x,
  language = AMR::get_AMR_locale(),
  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
  ...
)

Arguments

x	any character (vector) that can be coerced to a valid microorganism code with as.mo(). Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see Examples.
language	language to translate text like "no growth", which defaults to the system language (see get_AMR_locale())
keep_synonyms	a logical to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is FALSE, which will return a note if old taxonomic names were processed. The default can be set with the package option AMR_keep_synonyms, i.e. options(AMR_keep_synonyms = TRUE) or options(AMR_keep_synonyms = FALSE).
...	other arguments passed on to as.mo(), such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'

Examples

mo_glims("E. coli")

library(dplyr, warn.conflicts = FALSE)
data.frame(mo = c("ESCCOL", "Staph aureus")) |>
  mutate(glims = mo_glims())
  
# even works for non-existing entries in AMR package
mo_glims("Streptococcus mitis/oralis")

if (require(AMR, warn.conflicts = FALSE)) {
  as.mo("Streptococcus mitis/oralis")
}
if (require("AMR")) {
  mo_genus("Streptococcus mitis/oralis")
}
if (require("AMR")) {
  mo_gramstain("Streptococcus mitis/oralis")
}

certe-medical-epidemiology/certetoolbox documentation built on April 17, 2025, 3:24 a.m.