diff options
Diffstat (limited to 'reproduce/analysis/make')
| -rw-r--r-- | reproduce/analysis/make/demo-plot.mk | 59 | ||||
| -rw-r--r-- | reproduce/analysis/make/format.mk (renamed from reproduce/analysis/make/analysis-1.mk) | 25 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-make.mk | 5 |
3 files changed, 71 insertions, 18 deletions
diff --git a/reproduce/analysis/make/demo-plot.mk b/reproduce/analysis/make/demo-plot.mk new file mode 100644 index 0000000..caf77af --- /dev/null +++ b/reproduce/analysis/make/demo-plot.mk @@ -0,0 +1,59 @@ +# Second step of analysis: +# Data for plot of number/fraction of tools per year. +# +# 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/>. + + + + +# Directory to host outputs +# ------------------------- +a2dir = $(texdir)/tools-per-year +$(a2dir):; mkdir $@ + + + + + +# Table for Figure 1C of Menke+20 +# ------------------------------- +a2mk20f1c = $(a2dir)/tools-per-year.txt +$(a2mk20f1c): $(mk20tab3) | $(a2dir) + + # Remove the (possibly) produced figure that is created from this + # table: it is created by LaTeX's TiKZ package, and includes + # multiple files with a fixed prefix. + rm -f $(tikzdir)/figure-tools-per-year* + + # Find the maximum number of papers. + awk '!/^#/{all[$$1]+=$$2; id[$$1]+=$$3} \ + END{ for(year in all) \ + print year, 100*id[year]/all[year], all[year] \ + }' $< \ + > $@ + + + + + +# Final LaTeX macro +$(mtexdir)/demo-plot.tex: $(a2mk20f1c) $(pconfdir)/menke-demo-year.conf + + # Find the first year (first column of first row) of data. + v=$$(awk 'NR==1{print $$1}' $(a2mk20f1c)) + echo "\newcommand{\menkefirstyear}{$$v}" > $@ + + # Find the number of papers in 1996. + v=$$(awk '$$1==$(menke-demo-year){print $$3}' $(a2mk20f1c)) + echo "\newcommand{\menkenumpapersdemocount}{$$v}" >> $@ + echo "\newcommand{\menkenumpapersdemoyear}{$(menke-demo-year)}" >> $@ diff --git a/reproduce/analysis/make/analysis-1.mk b/reproduce/analysis/make/format.mk index f739306..868c411 100644 --- a/reproduce/analysis/make/analysis-1.mk +++ b/reproduce/analysis/make/format.mk @@ -1,7 +1,10 @@ -# Use the data from Menke 2020 (DOI:10.1101/2020.01.15.908111) as a -# demonstration analysis for this paper. This is a relevant paper because -# it provides good statistics about the status of reproducibility in -# scientific publications. +# First step of analysis: +# Prepare the data, return basic values. +# +# As a demonstration analysis to go with the paper, we use the data from +# Menke 2020 (DOI:10.1101/2020.01.15.908111). This is a relevant paper +# because it provides interesting statistics about tools and methods used +# in scientific papers. # # Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> # @@ -20,7 +23,7 @@ # Save the "Table 3" spreadsheet from the downloaded `.xlsx' file into a # simple plain-text file that is easy to use. -a1dir = $(BDIR)/analysis-1 +a1dir = $(BDIR)/analysis1 mk20tab3 = $(a1dir)/menke20-table-3.txt $(a1dir):; mkdir $@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir) @@ -61,19 +64,9 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir) -############################ -# Recreate Figure 1C of Menke+20. -############################ - -# awk '!/^#/{all[$1]+=$2; id[$1]+=$3} END{for(year in all){print year, id[year]/all[year]}}' menke20-table-3.txt.tmp -############################ - - - - # Main LaTeX macro file -$(mtexdir)/analysis-1.tex: $(mk20tab3) | $(mtexdir) +$(mtexdir)/format.tex: $(mk20tab3) # Count the total number of papers in their study. v=$$(awk '!/^#/{c+=$$2} END{print c}' $(mk20tab3)) diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 6dd322f..000c1fd 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -112,8 +112,9 @@ endif # wild-card like the configuration Makefiles). makesrc = initialize \ download \ + format \ + demo-plot \ verify \ - analysis-1 \ paper @@ -132,5 +133,5 @@ makesrc = initialize \ # But before that, we need to identify the phase for the Makefiles that are # run both in `./project prepare' and `./project make'. project-phase = make -include reproduce/analysis/config/*.mk +include reproduce/analysis/config/*.conf include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk) |