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https://github.com/msberends/AMR.git
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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper
This commit is contained in:
@ -40,262 +40,115 @@
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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(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_name(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_fullname(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_shortname(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_subspecies(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_species(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_genus(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_family(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_order(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_class(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_phylum(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_kingdom(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_domain(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_type(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_status(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_status(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_pathogenicity(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_pathogenicity(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_gramstain(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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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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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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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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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_is_yeast(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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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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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_oxygen_tolerance(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_oxygen_tolerance(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_is_anaerobic(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_is_anaerobic(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_snomed(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_ref(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_authors(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_year(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_lpsn(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_mycobank(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_mycobank(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_gbif(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_rank(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_taxonomy(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_synonyms(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_current(x, language = get_AMR_locale(), ...)
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mo_group_members(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_group_members(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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...
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)
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mo_info(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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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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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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", FALSE),
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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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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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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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Block a user