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# Use the data from Menke 2020 (DOI:10.1101/2020.01.15.908111) as a
# demonstration analysis for this paper. This is a relevant paper because
# it provides good statistics about the status of reproducibility in
# scientific publications.
#
# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# This Makefile is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.
#
# This Makefile is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details. See <http://www.gnu.org/licenses/>.
# Save the "Table 3" spreadsheet from the downloaded `.xlsx' file into a
# simple plain-text file that is easy to use.
mk20dir = $(BDIR)/menke2020
mk20tab3 = $(mk20dir)/table-3.txt
$(mk20dir):; mkdir $@
$(mk20tab3): $(indir)/menke-etal-2020.xlsx | $(mk20dir)
# Set a base-name for the table-3 data.
base=$(basename $(notdir $<))-table-3
# Unfortunately XLSX I/O only works when the input and output are
# in the directory it is running. So first, we need to switch to
# the input directory, run it, then put our desired output where we
# want and delete the extra files.
topdir=$$(pwd)
cd $(indir)
xlsxio_xlsx2csv $(notdir $<)
cp $(notdir $<)."Table 3 All by journal by year".csv $$base.csv
rm $(notdir $<).*.csv
cd $$topdir
# Read the necessary information. Note that we are dealing with a
# CSV (comma-separated value) file. But when there are commas in a
# string, quotation signs are put around it. The `FPAT' values is
# fully described in the GNU AWK manual. In short, it ensures that
# if there is a comma in the middle of double-quotes, it doesn't
# count as a delimter.
echo "# Column 1: YEAR [counter, i16] Year of journal's publication." > $@.tmp
echo "# Column 2: NUM_PAPERS [counter, i16] Number of studied papers in that journal." >> $@.tmp
echo "# Column 3: NUM_ID_TOOLS [counter, i16] Number of software/tools that were identified." >> $@.tmp
awk 'NR>1{printf("%-6d%-5d%d\n", $$2, $$3, $$(NF-1)*$$NF)}' \
FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp
# Set the temporary file as the final target. This was done so if
# there is any possible crash in the steps above, this rule is
# re-run (its final target isn't rebuilt).
mv $@.tmp $@
# Main LaTeX macro file
$(mtexdir)/menke2020.tex: $(mk20tab3) | $(mtexdir)
touch $@
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