mirror of https://github.com/msberends/AMR.git
58 lines
3.3 KiB
R
Executable File
58 lines
3.3 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Export Data Set as NCBI BioSample Antibiogram
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#'
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#'
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#' @param x a data set
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#' @param filename a character string specifying the file name
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#' @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/>
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#' @keywords internal
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export_ncbi_biosample <- function(x,
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filename = paste0("biosample_", format(Sys.time(), "%Y-%m-%d-%H%M%S"), ".xlsx"),
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type = "pathogen MIC",
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columns = where(is.mic),
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save_as_xlsx = TRUE) {
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meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
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meet_criteria(filename, allow_class = "character", has_length = 1)
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("pathogen MIC", "beta-lactamase MIC"))
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meet_criteria(save_as_xlsx, allow_class = "logical", has_length = 1)
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out <- x %pm>%
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pm_select(columns)
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stop_if(NROW(out) == 0, "No columns found.")
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if (isTRUE(save_as_xlsx)) {
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export <- import_fn("write.xlsx", pkg = "openxlsx", error_on_fail = TRUE)
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export(out, file = filename, overwrite = TRUE, asTable = FALSE)
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} else {
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out
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}
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}
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