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fix for antibiograms on R < 3.5

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dr. M.S. (Matthijs) Berends
2023-02-24 09:43:10 +01:00
parent e70f2cd32c
commit 049baf0a71
13 changed files with 108 additions and 101 deletions
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12
R/bug_drug_combinations.R
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@ -39,7 +39,7 @@
#' @param ... arguments passed on to `FUN`
#' @inheritParams sir_df
#' @inheritParams base::formatC
#' @details The function [format()] calculates the resistance per bug-drug combination. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S.
#' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
#' @export
#' @rdname bug_drug_combinations
#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
@ -327,7 +327,15 @@ format.bug_drug_combinations <- function(x,
}
rownames(y) <- NULL
as_original_data_class(y, class(x.bak)) # will remove tibble groups
as_original_data_class(y, class(x.bak), extra_class = "formatted_bug_drug_combinations") # will remove tibble groups
}
# will be exported in zzz.R
knit_print.formatted_bug_drug_combinations <- function(x, ...) {
stop_ifnot_installed("knitr")
# make columns with MO names italic according to nomenclature
colnames(x)[3:NCOL(x)] <- italicise_taxonomy(colnames(x)[3:NCOL(x)], type = "markdown")
knitr::asis_output(paste("", "", knitr::kable(x, ...), collapse = "\n"))
}
#' @method print bug_drug_combinations