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(v2.1.1.9099) fix generating GPT training test
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Package: AMR
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Version: 2.1.1.9098
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Version: 2.1.1.9099
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Date: 2024-10-17
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 2.1.1.9098
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# AMR 2.1.1.9099
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*(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! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
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#!/bin/bash
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# Check if the current directory is named 'AMR'
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if [ "$(basename "$PWD")" != "AMR" ]; then
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echo "Error: The script must be run from the 'AMR' directory."
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exit 1
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fi
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# Define the output file, located in ./data-raw
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output_file="gpt_training_text.txt"
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output_file="data-raw/gpt_training_text.txt"
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# Clear the output file if it exists
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echo "This files contains all context you must know about the AMR package for R."> "$output_file"
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@ -12,16 +18,16 @@ remove_header() {
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sed '/# =\{6,\}/,/# =\{6,\}/d' "$1"
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}
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# Process all .R files in the '../R' folder
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for file in ../R/*.R; do
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# Process all .R files in the 'R' folder
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for file in R/*.R; do
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echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# Process all .Rmd files in the '../vignettes' folder
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for file in ../vignettes/*.Rmd; do
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# Process all .Rmd files in the 'vignettes' folder
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for file in vignettes/*.Rmd; do
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echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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@ -29,7 +35,7 @@ for file in ../vignettes/*.Rmd; do
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done
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# Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
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for file in ../DESCRIPTION ../NAMESPACE ../index.md; do
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for file in DESCRIPTION NAMESPACE index.md; do
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if [[ -f $file ]]; then
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echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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@ -38,16 +44,16 @@ for file in ../DESCRIPTION ../NAMESPACE ../index.md; do
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fi
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done
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# Process test files (if available) in the '../tests' folder
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for file in ../tests/*.R; do
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# Process test files (if available) in the 'tests' folder
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for file in tests/*.R; do
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echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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done
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# Process all .Rd files from the '../man' folder
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for file in ../man/*.Rd; do
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# Process all .Rd files from the 'man' folder
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for file in man/*.Rd; do
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echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
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echo -e "\n\n" >> "$output_file"
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remove_header "$file" >> "$output_file"
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