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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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329
man/mo_property.Rd
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@@ -41,119 +41,270 @@
\alias{mo_url}
\title{Get Properties of a Microorganism}
\usage{
mo_name(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_fullname(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_shortname(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_subspecies(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_species(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_genus(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_family(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_order(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_class(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_phylum(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_kingdom(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_domain(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_type(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_status(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_pathogenicity(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_gramstain(x, language = get_AMR_locale(),
mo_name(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
add_morphology = FALSE, ...)
...
)
mo_is_gram_negative(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_fullname(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_gram_positive(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_shortname(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_yeast(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_subspecies(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_species(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_oxygen_tolerance(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_genus(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_anaerobic(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_family(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_morphology(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_order(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_snomed(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_class(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_ref(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_phylum(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_authors(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_kingdom(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_year(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_domain(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_lpsn(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_type(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_mycobank(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_status(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_gbif(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_pathogenicity(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_rank(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_gramstain(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
add_morphology = FALSE,
...
)
mo_taxonomy(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_gram_negative(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_synonyms(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_gram_positive(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_yeast(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_intrinsic_resistant(
x,
ab,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_oxygen_tolerance(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_anaerobic(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_morphology(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_snomed(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_ref(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_authors(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_year(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_lpsn(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_mycobank(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_gbif(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_rank(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_taxonomy(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_synonyms(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_current(x, language = get_AMR_locale(), ...)
mo_group_members(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_group_members(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_info(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_info(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_url(x, open = FALSE, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_url(
x,
open = FALSE,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_property(x, property = "fullname", language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_property(
x,
property = "fullname",
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
}
\arguments{
\item{x}{Any \link{character} (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}