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(v1.7.1.9011) subsetting taxonomy fix

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dr. M.S. (Matthijs) Berends
2021-07-04 15:26:50 +02:00
parent 3bd50710e8
commit 5b5741f681
20 changed files with 94 additions and 86 deletions
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2
R/bug_drug_combinations.R
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@ -25,7 +25,7 @@
#' Determine Bug-Drug Combinations
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see *Examples*.
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
#' @inheritSection lifecycle Stable Lifecycle
#' @inheritParams eucast_rules
#' @param combine_IR a [logical] to indicate whether values R and I should be summed

13
R/mo_property.R
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@ -48,11 +48,13 @@
#'
#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
#'
#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()].
#'
#' All output [will be translated][translate] where possible.
#'
#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
#'
#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info.
#' @inheritSection mo_matching_score Matching Score for Microorganisms
#' @inheritSection catalogue_of_life Catalogue of Life
#' @inheritSection as.mo Source
@ -63,9 +65,10 @@
#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
#' - A named [character] in case of [mo_url()]
#' - A [numeric] in case of [mo_snomed()]
#' - A [character] with additional class `taxonomic_name` in case of [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()]
#' - A [character] in all other cases
#' @export
#' @seealso [microorganisms]
#' @seealso Data set [microorganisms]
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @examples
@ -783,15 +786,15 @@ print.taxonomic_name <- function(x, ...) {
as.data.frame.taxonomic_name <- function(x, ...) {
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(x, ..., nm = nm)
as.data.frame(unclass(x), ..., nm = nm)
} else {
as.data.frame.vector(x, ...)
as.data.frame(unclass(x), ...)
}
}
# will be exported using s3_register() in R/zzz.R
type_sum.taxonomic_name <- function(x, ...) {
"chr"
"chr/taxon"
}
# will be exported using s3_register() in R/zzz.R