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(v3.0.1.9066) fix documentation

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dr. M.S. (Matthijs) Berends
2026-06-24 19:34:47 +02:00
parent 39b6a250de
commit a88150ca4a
7 changed files with 38 additions and 28 deletions
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5
R/data.R
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@@ -143,11 +143,10 @@
#' ### Manual additions
#' For convenience, some entries were added manually:
#'
#' - All `r format_included_data_number(length(which(microorganisms$rank == "species group")))` groups and complexes of the [microorganisms.groups] data set, for cross-reference (examples include beta-haemolytic *Streptococcus* groups A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium tuberculosis* complex, etc.)
#' - `r format_included_data_number(microorganisms[which(microorganisms$source == "manually added" & microorganisms$genus == "Salmonella"), , drop = FALSE])` entries of *Salmonella*, such as the city-like serovars and groups A to H
#' - `r format_included_data_number(length(which(microorganisms$rank == "species group")))` species groups (such as the beta-haemolytic *Streptococcus* groups A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium tuberculosis* complex, etc.), of which the group compositions are stored in the [microorganisms.groups] data set
#' - 1 entry of *Blastocystis* (*B. hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
#' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
#' - 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
#' - `r sum(microorganisms$fullname %like% "unknown")` other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
#'
#' The syntax used to transform the original data to a cleansed \R format, can be [found here](https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R).
#' @inheritSection AMR Download Our Reference Data

32
R/mo_property.R
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@@ -83,6 +83,7 @@
#' @examples
#' # taxonomic tree -----------------------------------------------------------
#'
#' mo_domain("Klebsiella pneumoniae")
#' mo_kingdom("Klebsiella pneumoniae")
#' mo_phylum("Klebsiella pneumoniae")
#' mo_class("Klebsiella pneumoniae")
@@ -92,6 +93,8 @@
#' mo_species("Klebsiella pneumoniae")
#' mo_subspecies("Klebsiella pneumoniae")
#'
#' # all in one go
#' mo_taxonomy("Klebsiella pneumoniae")
#'
#' # full names and short names -----------------------------------------------
#'
@@ -112,6 +115,7 @@
#' mo_url("Klebsiella pneumoniae")
#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
#'
#' mo_group_members("Streptococcus group A")
#' mo_group_members(c(
#' "Streptococcus group A",
#' "Streptococcus group C",
@@ -155,6 +159,7 @@
#'
#' mo_fullname("Staph epidermidis")
#' mo_fullname("Staph epidermidis", Becker = TRUE)
#'
#' mo_shortname("Staph epidermidis")
#' mo_shortname("Staph epidermidis", Becker = TRUE)
#'
@@ -163,6 +168,7 @@
#'
#' mo_fullname("Strep agalactiae")
#' mo_fullname("Strep agalactiae", Lancefield = TRUE)
#'
#' mo_shortname("Strep agalactiae")
#' mo_shortname("Strep agalactiae", Lancefield = TRUE)
#'
@@ -175,10 +181,10 @@
#' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
#' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#'
#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
#' mo_kingdom("Klebsiella pneumoniae")
#' # mo_type is equal to mo_domain, but mo_domain will remain untranslated
#' mo_domain("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae")
#' mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#' mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#' mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#'
#' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
@@ -807,19 +813,19 @@ mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
metadata <- get_mo_uncertainties()
out <- list(
domain = mo_domain(x, language = language, keep_synonyms = keep_synonyms),
kingdom = mo_kingdom(x, language = language, keep_synonyms = keep_synonyms),
phylum = mo_phylum(x, language = language, keep_synonyms = keep_synonyms),
class = mo_class(x, language = language, keep_synonyms = keep_synonyms),
order = mo_order(x, language = language, keep_synonyms = keep_synonyms),
family = mo_family(x, language = language, keep_synonyms = keep_synonyms),
genus = mo_genus(x, language = language, keep_synonyms = keep_synonyms),
species = mo_species(x, language = language, keep_synonyms = keep_synonyms),
subspecies = mo_subspecies(x, language = language, keep_synonyms = keep_synonyms)
domain = mo_domain(x.mo, language = language, keep_synonyms = keep_synonyms),
kingdom = suppressMessages(mo_kingdom(x.mo, language = language, keep_synonyms = keep_synonyms)),
phylum = mo_phylum(x.mo, language = language, keep_synonyms = keep_synonyms),
class = mo_class(x.mo, language = language, keep_synonyms = keep_synonyms),
order = mo_order(x.mo, language = language, keep_synonyms = keep_synonyms),
family = mo_family(x.mo, language = language, keep_synonyms = keep_synonyms),
genus = mo_genus(x.mo, language = language, keep_synonyms = keep_synonyms),
species = mo_species(x.mo, language = language, keep_synonyms = keep_synonyms),
subspecies = mo_subspecies(x.mo, language = language, keep_synonyms = keep_synonyms)
)
load_mo_uncertainties(metadata)