fix unit test

.github/prehooks/pre-commit

@@ -36,10 +36,10 @@
 # try to fetch the commit message from the standard location
 COMMIT_MSG_PATH=".git/COMMIT_EDITMSG"
 if [ -f "$COMMIT_MSG_PATH" ]; then
-    COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
+  COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
 else
-    echo "Commit message file not found."
+  echo "Commit message file not found."
-    echo 1
+  COMMIT_MSG=""
 fi
 # check the commit message, cancel commit if needed
 if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
@@ -118,4 +118,15 @@ if [ -e "NEWS.md" ]; then
 else
   echo "- no NEWS.md found!"
 fi
+
+# Prepend the version number to the commit message
+if [ -f "$COMMIT_MSG_PATH" ]; then
+  # Prepend the version number
+  echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_PATH"
+  echo "- prepended version number to commit message"
+else
+  echo ""
+  echo "Commit message file not found. Unable to prepend version number."
+fi
+
 echo ""

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9037
+Version: 2.1.1.9038
-Date: 2024-05-31
+Date: 2024-06-04
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9037
+# AMR 2.1.1.9038
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
 

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",

index.md

@@ -1,16 +1,18 @@
 # The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
 
+<img src="./endorsement_clsi_eucast.jpg" align="right" height="120" />
+
 * Provides an **all-in-one solution** for AMR data analysis in a One Health approach
 * Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
-* Provides the **full microbiological taxonomy** and data on **all antimicrobial drugs**
+* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
-* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for  MICs and disk zones
+* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for MICs and disk zones
 * Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
-* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, and **SNOMED CT**
+* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
 * Works on Windows, macOS and Linux with **all versions of R** since R-3.0 and is completely **dependency-free**, highly suitable for places with **limited resources**
 
 <div style="display: flex; font-size: 0.8em;">
 <p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
-<p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03">https://doi.org/10.18637/jss.v104.i03</a></small></p>
+<p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small></p>
 </div>
 
 ----
@@ -25,7 +27,7 @@ After installing this package, R knows [**~52,000 distinct microbial species**](
 
 ##### Used in over 175 countries, translated into 20 languages
 
-<a href="./countries_large.png"><img src="./countries.png" target="_blank" align="right" style="max-width: 300px;" /></a>
+<a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;" /></a>
 
 Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
 

man/export_biosample.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/export_biosample.R
+\name{export_biosample}
+\alias{export_biosample}
+\title{Export Data Set as NCBI BioSample Antibiogram}
+\usage{
+export_biosample(
+  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
+)
+}
+\arguments{
+\item{x}{a data set}
+
+\item{filename}{a character string specifying the file name}
+
+\item{type}{a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see \url{https://www.ncbi.nlm.nih.gov/biosample/docs/}}
+}
+\description{
+Export Data Set as NCBI BioSample Antibiogram
+}