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fixes
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.1.9057
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Version: 1.8.1.9058
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Date: 2022-09-19
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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@ -270,6 +270,7 @@ export(mo_domain)
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export(mo_failures)
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export(mo_family)
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export(mo_fullname)
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export(mo_gbif)
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export(mo_genus)
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export(mo_gramstain)
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export(mo_info)
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.1.9057
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# AMR 1.8.1.9058
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -476,10 +476,8 @@ invisible(capture.output(urlchecker::url_update()))
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# Document pkg ------------------------------------------------------------
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if (interactive()) {
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usethis::ui_info("Documenting package")
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suppressMessages(devtools::document(quiet = TRUE))
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}
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# Style pkg ---------------------------------------------------------------
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@ -16,9 +16,9 @@ as.mo(
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Lancefield = FALSE,
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minimum_matching_score = NULL,
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allow_uncertain = TRUE,
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keep_synonyms = FALSE,
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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reference_df = get_mo_source(),
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ignore_pattern = getOption("AMR_ignore_pattern"),
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ignore_pattern = getOption("AMR_ignore_pattern", NULL),
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language = get_AMR_locale(),
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info = interactive(),
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...
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@ -49,7 +49,7 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
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\item{allow_uncertain}{a number between \code{0} (or \code{"none"}) and \code{3} (or \code{"all"}), or \code{TRUE} (= \code{2}) or \code{FALSE} (= \code{0}) to indicate whether the input should be checked for less probable results, see \emph{Details}}
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\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE} to always return the currently accepted names.}
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\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{TRUE}, which will return a note if old taxonomic names are returned. The default can be set with \code{options(AMR_keep_synonyms = ...)}.}
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\item{reference_df}{a \link{data.frame} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
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@ -25,6 +25,7 @@
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\alias{mo_authors}
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\alias{mo_year}
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\alias{mo_lpsn}
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\alias{mo_gbif}
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\alias{mo_rank}
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\alias{mo_taxonomy}
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\alias{mo_synonyms}
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@ -32,68 +33,225 @@
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\alias{mo_url}
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\title{Get Properties of a Microorganism}
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\usage{
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mo_name(x, language = get_AMR_locale(), ...)
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mo_name(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_fullname(x, language = get_AMR_locale(), ...)
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mo_fullname(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_shortname(x, language = get_AMR_locale(), ...)
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mo_shortname(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_subspecies(x, language = get_AMR_locale(), ...)
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mo_subspecies(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_species(x, language = get_AMR_locale(), ...)
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mo_species(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_genus(x, language = get_AMR_locale(), ...)
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mo_genus(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_family(x, language = get_AMR_locale(), ...)
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mo_family(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_order(x, language = get_AMR_locale(), ...)
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mo_order(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_class(x, language = get_AMR_locale(), ...)
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mo_class(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_phylum(x, language = get_AMR_locale(), ...)
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mo_phylum(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_kingdom(x, language = get_AMR_locale(), ...)
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mo_kingdom(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_domain(x, language = get_AMR_locale(), ...)
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mo_domain(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_type(x, language = get_AMR_locale(), ...)
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mo_type(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_gramstain(x, language = get_AMR_locale(), ...)
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mo_gramstain(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_is_gram_negative(x, language = get_AMR_locale(), ...)
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mo_is_gram_negative(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_is_gram_positive(x, language = get_AMR_locale(), ...)
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mo_is_gram_positive(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_is_yeast(x, language = get_AMR_locale(), ...)
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mo_is_yeast(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(), ...)
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mo_is_intrinsic_resistant(
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x,
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ab,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_snomed(x, language = get_AMR_locale(), ...)
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mo_snomed(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_ref(x, language = get_AMR_locale(), ...)
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mo_ref(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_authors(x, language = get_AMR_locale(), ...)
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mo_authors(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_year(x, language = get_AMR_locale(), ...)
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mo_year(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_lpsn(x, language = get_AMR_locale(), ...)
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mo_lpsn(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_rank(x, language = get_AMR_locale(), ...)
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mo_gbif(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_taxonomy(x, language = get_AMR_locale(), ...)
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mo_rank(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_synonyms(x, language = get_AMR_locale(), ...)
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mo_taxonomy(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_info(x, language = get_AMR_locale(), ...)
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mo_synonyms(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_url(x, open = FALSE, language = get_AMR_locale(), ...)
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mo_info(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_property(x, property = "fullname", language = get_AMR_locale(), ...)
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mo_url(
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x,
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open = FALSE,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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mo_property(
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x,
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property = "fullname",
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
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...
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)
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}
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\arguments{
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\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}.}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
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\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{TRUE}, which will return a note if old taxonomic names are returned. The default can be set with \code{options(AMR_keep_synonyms = ...)}.}
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\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'allow_uncertain' and 'ignore_pattern'}
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@ -116,7 +274,7 @@ mo_property(x, property = "fullname", language = get_AMR_locale(), ...)
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Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with \code{\link[=as.mo]{as.mo()}}, which makes it possible to use microbial abbreviations, codes and names as input. See \emph{Examples}.
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}
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\details{
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All functions will return the most recently known taxonomic property \link[=microorganisms]{as included in this package}, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{mo_year()}}. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
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All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
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\itemize{
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\item \code{mo_name("Escherichia blattae")} will return \code{"Shimwellia blattae"} (with a message about the renaming)
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\item \code{mo_ref("Escherichia blattae")} will return \code{"Burgess et al., 1973"} (with a message about the renaming)
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