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.

1 files changed, 0 insertions, 78 deletions

diff --git a/reproduce/analysis/make/menke2020.mk b/reproduce/analysis/make/menke2020.mk
deleted file mode 100644
index 4dd9897..0000000
--- a/reproduce/analysis/make/menke2020.mk
+++ /dev/null
@@ -1,78 +0,0 @@
-# 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 $$topdir
-
-        # Read the necessary information. Note that we are dealing with a
-        # CSV (comma-separated value) file. But when there are commas in a
-        # string, quotation signs are put around it. The `FPAT' values is
-        # fully described in the GNU AWK manual. In short, it ensures that
-        # if there is a comma in the middle of double-quotes, it doesn't
-        # count as a delimter.
-	echo "# Column 1: YEAR [counter, i16] Year of journal's publication." > $@.tmp
-	echo "# Column 2: NUM_PAPERS [counter, i16] Number of studied papers in that journal." >> $@.tmp
-	echo "# Column 3: NUM_ID_TOOLS [counter, i16] Number of software/tools that were identified." >> $@.tmp
-	echo "# Column 4: JOURNAL_NAME [string, str150] Name of journal." >> $@.tmp
-	awk 'NR>1{printf("%-10d%-10d%-10d %s\n", $$2, $$3, $$(NF-1)*$$NF, $$1)}' \
-	    FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp
-
-        # Set the temporary file as the final target. This was done so if
-        # there is any possible crash in the steps above, this rule is
-        # re-run (its final target isn't rebuilt).
-	mv $@.tmp $@
-
-
-
-
-
-# Main LaTeX macro file
-$(mtexdir)/menke2020.tex: $(mk20tab3) | $(mtexdir)
-
-        # Count the total number of papers in their study.
-	v=$$(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}" >> $@