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commit 46858ec0a2
114 changed files with 478 additions and 358 deletions

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@@ -180,8 +180,9 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
- An [integer](https://rdrr.io/r/base/integer.html) in case of
`mo_year()`
- An [ordered factor](https://rdrr.io/r/base/factor.html) in case of
`mo_pathogenicity()`
- An [ordered
factor](https://rdatatable.gitlab.io/data.table/reference/fctr.html)
in case of `mo_pathogenicity()`
- A [list](https://rdrr.io/r/base/list.html) in case of `mo_taxonomy()`,
`mo_synonyms()`, `mo_snomed()`, and `mo_info()`
@@ -238,9 +239,10 @@ Since the top-level of the taxonomy is sometimes referred to as
Determination of human pathogenicity (`mo_pathogenicity()`) is strongly
based on Bartlett *et al.* (2022,
[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ). This
function returns a [factor](https://rdrr.io/r/base/factor.html) with the
levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and
*Unknown*.
function returns a
[factor](https://rdatatable.gitlab.io/data.table/reference/fctr.html)
with the levels *Pathogenic*, *Potentially pathogenic*,
*Non-pathogenic*, and *Unknown*.
Determination of the Gram stain (`mo_gramstain()`) will be based on the
taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
@@ -540,15 +542,15 @@ mo_shortname("Strep agalactiae", Lancefield = TRUE)
# language support --------------------------------------------------------
mo_gramstain("Klebsiella pneumoniae", language = "de") # German
#> [1] "Gramnegativ"
#> [1] "Gram-negative"
mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
#> [1] "Gram-negatief"
#> [1] "Gram-negative"
mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
#> [1] "Gram negativo"
#> [1] "Gram-negative"
mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
#> [1] "Αρνητικό κατά Gram"
#> [1] "Gram-negative"
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#> [1] "Грамнегативні"
#> [1] "Gram-negative"
# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
mo_kingdom("Klebsiella pneumoniae")
@@ -558,7 +560,7 @@ mo_type("Klebsiella pneumoniae")
mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#> [1] "细菌"
#> [1] "Bacteria"
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
#> [1] "Streptococcus Gruppe A"