fix unit test

R/export_biosample.R

@@ -0,0 +1,57 @@
+# ==================================================================== #
+# 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/>
+#' @param save_as_xlsx
+export_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) {
+  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
+  }
+}

R/sir.R

@@ -858,6 +858,8 @@ as_sir_method <- function(method_short,
         }
       )
     }
+  } else {
+    mo_var_found <- ""
   }
   if (is.null(mo)) {
     stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class 'mo' found). See ?as.sir.\n\n",