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(v2.1.1.9279) fix documentation, add foreign S3 exports to functions

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dr. M.S. (Matthijs) Berends
2025-05-16 16:55:29 +02:00
parent 139f79d372
commit 38cebc1541
24 changed files with 292 additions and 239 deletions
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12
R/antibiogram.R
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@ -1190,7 +1190,8 @@ retrieve_wisca_parameters <- function(wisca_model, ...) {
attributes(wisca_model)$wisca_parameters
}
# will be exported in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_sum, antibiogram)
tbl_sum.antibiogram <- function(x, ...) {
dims <- paste(format(NROW(x), big.mark = ","), AMR_env$cross_icon, format(NCOL(x), big.mark = ","))
if (isTRUE(attributes(x)$wisca)) {
@ -1203,7 +1204,8 @@ tbl_sum.antibiogram <- function(x, ...) {
dims
}
# will be exported in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_format_footer, antibiogram)
tbl_format_footer.antibiogram <- function(x, ...) {
footer <- NextMethod()
if (NROW(x) == 0) {
@ -1271,7 +1273,8 @@ barplot.antibiogram <- function(height, ...) {
#' @method autoplot antibiogram
#' @rdname antibiogram
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, antibiogram)
autoplot.antibiogram <- function(object, ...) {
df <- attributes(object)$long_numeric
if (!"mo" %in% colnames(df)) {
@ -1318,11 +1321,12 @@ autoplot.antibiogram <- function(object, ...) {
out
}
# will be exported in zzz.R
#' @method knit_print antibiogram
#' @param italicise A [logical] to indicate whether the microorganism names in the [knitr][knitr::kable()] table should be made italic, using [italicise_taxonomy()].
#' @param na Character to use for showing `NA` values.
#' @rdname antibiogram
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(knitr::knit_print, antibiogram)
knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) {
stop_ifnot_installed("knitr")
meet_criteria(italicise, allow_class = "logical", has_length = 1)