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(v1.2.0.9011) mo_domain(), improved error handling

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dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
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27
R/mo_property.R
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@ -28,14 +28,16 @@
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
#' @param ... other parameters passed on to [as.mo()]
#' @param open browse the URL using [utils::browseURL()]
#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. This leads to the following results:
#' - `mo_name("Chlamydia psittaci")` will return `"Chlamydophila psittaci"` (with a warning about the renaming)
#' - `mo_ref("Chlamydia psittaci")` will return `"Page, 1968"` (with a warning about the renaming)
#' - `mo_ref("Chlamydophila psittaci")` will return `"Everett et al., 1999"` (without a warning)
#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010:
#' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming)
#' - `mo_ref("Escherichia blattae")` will return `"Burgess et al., 1973"` (with a message about the renaming)
#' - `mo_ref("Shimwellia blattae")` will return `"Priest et al., 2010"` (without a message)
#'
#' The short name - [mo_shortname()] - almost always returns the first character of the genus and the full species, like *"E. coli"*. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like *"CoNS"* (Coagulase-Negative Staphylococci) and *"GBS"* (Group B Streptococci).
#' The short name - [mo_shortname()] - almost always returns the first character of the genus and the full species, like `"E. coli"`. Exceptions are abbreviations of staphylococci (like *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. In other words, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.
#'
#' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.
#'
#' The Gram stain - [mo_gramstain()] - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`.
#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`.
#'
#' All output will be [translate]d where possible.
#'
@ -218,6 +220,10 @@ mo_kingdom <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_domain <- mo_kingdom
#' @rdname mo_property
#' @export
mo_type <- function(x, language = get_locale(), ...) {
@ -391,12 +397,9 @@ mo_url <- function(x, open = FALSE, ...) {
#' @rdname mo_property
#' @export
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
if (length(property) != 1L) {
stop("'property' must be of length 1.")
}
if (!property %in% colnames(microorganisms)) {
stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
}
stop_ifnot(length(property) == 1L, "'property' must be of length 1")
stop_ifnot(property %in% colnames(microorganisms),
"invalid property: '", property, "' - use a column name of the `microorganisms` data set")
translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
}