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# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Export Data Set as NCBI BioSample Antibiogram
#'
#'
#' @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/>
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#' @keywords internal
export_ncbi_biosample <- function ( x ,
filename = paste0 ( " biosample_" , format ( Sys.time ( ) , " %Y-%m-%d-%H%M%S" ) , " .xlsx" ) ,
type = " pathogen MIC" ,
columns = where ( is.mic ) ,
save_as_xlsx = TRUE ) {
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meet_criteria ( x , allow_class = " data.frame" ) # also checks dimensions to be >0
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 )
} else {
out
}
}