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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 18:46:11 +01:00

fix unit test

This commit is contained in:
dr. M.S. (Matthijs) Berends 2024-06-04 20:17:54 +02:00
parent 7c1b564648
commit c5981cdeb3
8 changed files with 107 additions and 11 deletions

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@ -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 "$COMMIT_MSG_PATH")
else
echo "Commit message file not found."
echo 1
echo "Commit message file not found."
COMMIT_MSG=""
fi
# check the commit message, cancel commit if needed
if [[ "$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 ""

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@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9037
Date: 2024-05-31
Version: 2.1.1.9038
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

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@ -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!)*

57
R/export_biosample.R Executable file
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@ -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
}
}

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@ -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",

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@ -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**
* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for MICs and disk zones
* 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
* 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.

24
man/export_biosample.Rd Normal file
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@ -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
}

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