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mirror of https://github.com/msberends/AMR.git synced 2025-09-06 04:49:36 +02:00

(v2.1.1.9163) cleanup

This commit is contained in:
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions

View File

@@ -29,8 +29,8 @@
#' Export Data Set as NCBI BioSample Antibiogram
#'
#'
#' @param x a data set
#'
#' @param x a data set
#' @param filename a character string specifying the file name
#' @param type a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <https://www.ncbi.nlm.nih.gov/biosample/docs/>
#' @keywords internal
@@ -43,11 +43,11 @@ export_ncbi_biosample <- function(x,
meet_criteria(filename, allow_class = "character", has_length = 1)
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("pathogen MIC", "beta-lactamase MIC"))
meet_criteria(save_as_xlsx, allow_class = "logical", has_length = 1)
out <- x %pm>%
pm_select(columns)
stop_if(NROW(out) == 0, "No columns found.")
if (isTRUE(save_as_xlsx)) {
export <- import_fn("write.xlsx", pkg = "openxlsx", error_on_fail = TRUE)
export(out, file = filename, overwrite = TRUE, asTable = FALSE)