This function is analogous to all mo_* functions of the AMR package, see AMR::mo_property().
mo_glims(
x,
language = AMR::get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)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 to translate text like "no growth", which defaults to the system language (see get_AMR_locale())
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'
mo_glims("E. coli")
#> [1] "Eschcl"
library(dplyr, warn.conflicts = FALSE)
data.frame(mo = c("ESCCOL", "Staph aureus")) |>
mutate(glims = mo_glims())
#> i Using column 'mo' as input for mo_name()
#> mo glims
#> 1 ESCCOL Eschcl
#> 2 Staph aureus Stphars
# even works for non-existing entries in AMR package
mo_glims("Streptococcus mitis/oralis")
#> [1] "Strpmi/or"
AMR::as.mo("Streptococcus mitis/oralis")
#> Class 'mo'
#> [1] CUSTOM615_STRPT_MTS/
AMR::mo_genus("Streptococcus mitis/oralis")
#> [1] "Streptococcus"
AMR::mo_gramstain("Streptococcus mitis/oralis")
#> [1] "Gram-positive"