From e9c81f9f40187bc4701ac539d110003e92b9ca69 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Mon, 2 Mar 2020 02:55:00 +0000 Subject: Described the first analysis phase with a demo subMakefile Until now, there was no explanation on an actual analysis phase, therefore with this commit an example scenario with a readable Makefile is included. The Data lineage graph was also simplified to both be more readable, and also to correspond to this new explanation and subMakefile. Some random edits/typos were also corrected and some references added for discussion. --- reproduce/analysis/make/analysis-1.mk | 78 +++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 reproduce/analysis/make/analysis-1.mk (limited to 'reproduce/analysis/make/analysis-1.mk') diff --git a/reproduce/analysis/make/analysis-1.mk b/reproduce/analysis/make/analysis-1.mk new file mode 100644 index 0000000..9d0018e --- /dev/null +++ b/reproduce/analysis/make/analysis-1.mk @@ -0,0 +1,78 @@ +# 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 +# +# 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 . + + + + +# Save the "Table 3" spreadsheet from the downloaded `.xlsx' file into a +# simple plain-text file that is easy to use. +a1dir = $(BDIR)/analysis-1 +mk20tab3 = $(a1dir)/menke20-table-3.txt +$(a1dir):; mkdir $@ +$(mk20tab3): $(indir)/menke20.xlsx | $(a1dir) + + # Set a base-name for the table-3 data. + base=$(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 $$topdir + + # Read the necessary information. Note that we are dealing with a + # CSV (comma-separated value) file. But when there are commas in a + # string, quotation signs are put around it. The `FPAT' values is + # fully described in the GNU AWK manual. In short, it ensures that + # if there is a comma in the middle of double-quotes, it doesn't + # count as a delimter. + echo "# Column 1: YEAR [counter, i16] Year of journal's publication." > $@.tmp + echo "# Column 2: NUM_PAPERS [counter, i16] Number of studied papers in that journal." >> $@.tmp + echo "# Column 3: NUM_ID_TOOLS [counter, i16] Number of software/tools that were identified." >> $@.tmp + echo "# Column 4: JOURNAL_NAME [string, str150] Name of journal." >> $@.tmp + awk 'NR>1{printf("%-10d%-10d%-10d %s\n", $$2, $$3, $$(NF-1)*$$NF, $$1)}' \ + FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp + + # Set the temporary file as the final target. This was done so if + # there is any possible crash in the steps above, this rule is + # re-run (its final target isn't rebuilt). + mv $@.tmp $@ + + + + + +# Main LaTeX macro file +$(mtexdir)/analysis-1.tex: $(mk20tab3) | $(mtexdir) + + # Count the total number of papers in their study. + v=$$(awk '!/^#/{c+=$$2} END{print c}' $(mk20tab3)) + echo "\newcommand{\menkenumpapers}{$$v}" > $@ + + # Count how many unique journals there were in the study. Note that + # the `31' comes because we put 10 characters for each numeric + # column and separated the last numeric column from the string + # column with a space. If the number of numeric columns change in + # the future, the `31' also has to change. + v=$$(awk 'BEGIN{FIELDWIDTHS="31 10000"} !/^#/{print $$2}' \ + $(mk20tab3) | uniq | wc -l) + echo "\newcommand{\menkenumjournals}{$$v}" >> $@ -- cgit v1.2.1