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2026-06-23 18:00:14 +00:00
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reference/add_custom_microorganisms.md
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@@ -121,15 +121,24 @@ mo_gramstain("Enterobacter asburiae/cloacae")
#> [1] "Gram-negative"
mo_info("Enterobacter asburiae/cloacae")
#> ℹ Since AMR v3.1.0, `mo_kingdom()` returns the taxonomic kingdom as defined by
#> Göker and Oren (2024), who formally introduced a new kingdom rank into
#> prokaryotic nomenclature (DOI: 10.1099/ijsem.0.006242
#> (<https://doi.org/10.1099/ijsem.0.006242>)). The former kingdom of Bacteria
#> was divided into four new kingdoms under the new domain of Bacteria. For the
#> old behaviour, use `mo_domain()`. This note will be shown once per session.
#> $mo
#> [1] "CUSTOM1_ENTRB_ASB/"
#>
#> $rank
#> [1] "species"
#>
#> $kingdom
#> $domain
#> [1] "Bacteria"
#>
#> $kingdom
#> [1] "Pseudomonadati"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
@@ -160,6 +169,9 @@ mo_info("Enterobacter asburiae/cloacae")
#> $gramstain
#> [1] "Gram-negative"
#>
#> $morphology
#> [1] NA
#>
#> $oxygen_tolerance
#> [1] NA
#>
@@ -215,9 +227,9 @@ add_custom_microorganisms(
#> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the
#> internal `microorganisms` data set.
mo_name(c("C. freundii complex", "C. braakii complex"))
#> [1] "Citrobacter freundii complex" "Citrobacter braakii complex"
#> [1] "Citrobacter freundii" "Citrobacter braakii"
mo_species(c("C. freundii complex", "C. braakii complex"))
#> [1] "freundii complex" "braakii complex"
#> [1] "freundii" "braakii"
mo_gramstain(c("C. freundii complex", "C. braakii complex"))
#> [1] "Gram-negative" "Gram-negative"
# }