# taxonomic tree -----------------------------------------------------------
+mo_domain("Klebsiella pneumoniae")
+#> [1] "Bacteria"
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Pseudomonadati"
mo_phylum("Klebsiella pneumoniae")
@@ -445,6 +447,35 @@
mo_subspecies("Klebsiella pneumoniae")
#> [1] ""
+# all in one go
+mo_taxonomy("Klebsiella pneumoniae")
+#> $domain
+#> [1] "Bacteria"
+#>
+#> $kingdom
+#> [1] "Pseudomonadati"
+#>
+#> $phylum
+#> [1] "Pseudomonadota"
+#>
+#> $class
+#> [1] "Gammaproteobacteria"
+#>
+#> $order
+#> [1] "Enterobacterales"
+#>
+#> $family
+#> [1] "Enterobacteriaceae"
+#>
+#> $genus
+#> [1] "Klebsiella"
+#>
+#> $species
+#> [1] "pneumoniae"
+#>
+#> $subspecies
+#> [1] ""
+#>
# full names and short names -----------------------------------------------
@@ -482,6 +513,8 @@
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
#> [1] TRUE FALSE FALSE
+mo_group_members("Streptococcus group A")
+#> [1] "Streptococcus pyogenes"
mo_group_members(c(
"Streptococcus group A",
"Streptococcus group C",
@@ -572,6 +605,7 @@
#> [1] "Staphylococcus epidermidis"
mo_fullname("Staph epidermidis", Becker = TRUE)
#> [1] "Coagulase-negative Staphylococcus (CoNS)"
+
mo_shortname("Staph epidermidis")
#> [1] "S. epidermidis"
mo_shortname("Staph epidermidis", Becker = TRUE)
@@ -584,6 +618,7 @@
#> [1] "Streptococcus agalactiae"
mo_fullname("Strep agalactiae", Lancefield = TRUE)
#> [1] "Streptococcus Group B"
+
mo_shortname("Strep agalactiae")
#> [1] "S. agalactiae"
mo_shortname("Strep agalactiae", Lancefield = TRUE)
@@ -603,13 +638,13 @@
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#> [1] "Грамнегативні"
-# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
-mo_kingdom("Klebsiella pneumoniae")
-#> [1] "Pseudomonadati"
+# mo_type is equal to mo_domain, but mo_domain will remain untranslated
+mo_domain("Klebsiella pneumoniae")
+#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae")
#> [1] "Bacteria"
-mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
-#> [1] "Pseudomonadati"
+mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
+#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#> [1] "细菌"
diff --git a/reference/mo_property.md b/reference/mo_property.md
index 89fc4712e..d329ad3e7 100644
--- a/reference/mo_property.md
+++ b/reference/mo_property.md
@@ -564,6 +564,8 @@ Data set
``` r
# taxonomic tree -----------------------------------------------------------
+mo_domain("Klebsiella pneumoniae")
+#> [1] "Bacteria"
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Pseudomonadati"
mo_phylum("Klebsiella pneumoniae")
@@ -581,6 +583,35 @@ mo_species("Klebsiella pneumoniae")
mo_subspecies("Klebsiella pneumoniae")
#> [1] ""
+# all in one go
+mo_taxonomy("Klebsiella pneumoniae")
+#> $domain
+#> [1] "Bacteria"
+#>
+#> $kingdom
+#> [1] "Pseudomonadati"
+#>
+#> $phylum
+#> [1] "Pseudomonadota"
+#>
+#> $class
+#> [1] "Gammaproteobacteria"
+#>
+#> $order
+#> [1] "Enterobacterales"
+#>
+#> $family
+#> [1] "Enterobacteriaceae"
+#>
+#> $genus
+#> [1] "Klebsiella"
+#>
+#> $species
+#> [1] "pneumoniae"
+#>
+#> $subspecies
+#> [1] ""
+#>
# full names and short names -----------------------------------------------
@@ -618,6 +649,8 @@ mo_url("Klebsiella pneumoniae")
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
#> [1] TRUE FALSE FALSE
+mo_group_members("Streptococcus group A")
+#> [1] "Streptococcus pyogenes"
mo_group_members(c(
"Streptococcus group A",
"Streptococcus group C",
@@ -708,6 +741,7 @@ mo_fullname("Staph epidermidis")
#> [1] "Staphylococcus epidermidis"
mo_fullname("Staph epidermidis", Becker = TRUE)
#> [1] "Coagulase-negative Staphylococcus (CoNS)"
+
mo_shortname("Staph epidermidis")
#> [1] "S. epidermidis"
mo_shortname("Staph epidermidis", Becker = TRUE)
@@ -720,6 +754,7 @@ mo_fullname("Strep agalactiae")
#> [1] "Streptococcus agalactiae"
mo_fullname("Strep agalactiae", Lancefield = TRUE)
#> [1] "Streptococcus Group B"
+
mo_shortname("Strep agalactiae")
#> [1] "S. agalactiae"
mo_shortname("Strep agalactiae", Lancefield = TRUE)
@@ -739,13 +774,13 @@ mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#> [1] "Грамнегативні"
-# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
-mo_kingdom("Klebsiella pneumoniae")
-#> [1] "Pseudomonadati"
+# mo_type is equal to mo_domain, but mo_domain will remain untranslated
+mo_domain("Klebsiella pneumoniae")
+#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae")
#> [1] "Bacteria"
-mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
-#> [1] "Pseudomonadati"
+mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
+#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#> [1] "细菌"
diff --git a/reference/mo_source.html b/reference/mo_source.html
index 16994029d..163476db3 100644
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
AMR (for R)
- 3.0.1.9065
+ 3.0.1.9067