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executable file 28 lines (22 sloc) 631 Bytes
#!/bin/sh
DIR="`dirname $0`"
# download XML
echo "Fetching PubMed XML..."
Rscript $DIR/scripts/fetchXML.R
echo "Finished."
# download total publications per year
echo "Fetching total publication counts by year..."
Rscript $DIR/scripts/byyear.R
echo "Finished."
# normalise retraction counts by journal
echo "Normalising retraction counts by journal..."
Rscript $DIR/scripts/byjournal.R
echo "Finished."
# knit the Rmd document
echo "Creating report..."
IN=$DIR/pmretract.Rmd
OUT="$DIR/../../../docs/pmretract/"
Rscript -e "library(rmarkdown); render('$IN', 'html_document')"
mv $DIR/pmretract.html $OUT
echo "Finished."
# git