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diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..2e6b333 --- /dev/null +++ b/Makefile @@ -0,0 +1,76 @@ +# Paper + +loael.pdf: loael.md references.bibtex + pandoc -r markdown+simple_tables+table_captions+yaml_metadata_block -s -S --bibliography=references.bibtex --latex-engine=pdflatex --filter pandoc-crossref --filter pandoc-citeproc -o loael.pdf loael.md + +loael.md: loael.Rmd figures # TODO: add further dependencies + Rscript --vanilla -e "library(knitr); knit('loael.Rmd');" + +loael.docx: loael.md + pandoc --filter pandoc-crossref --filter pandoc-citeproc loael.md -s -o loael.docx + +# Figures + +figures: datasets validations figure/functional-groups.pdf figure/test-prediction.pdf figure/test-correlation.pdf figure/crossvalidation.pdf figure/dataset-variability.pdf + +figure/functional-groups.pdf: data/functional-groups-reduced4R.csv functional-groups.R + Rscript functional-groups.R +figure/dataset-variability.pdf: data/mazzatorta.csv data/swiss.csv dataset-variability.R + Rscript dataset-variability.R + +figure/crossvalidation.pdf: data/combined-cv.csv + Rscript crossvalidation-plots.R + +figure/test-prediction.pdf: data/combined-test-predictions.csv data/median-correlation.csv test-prediction-plot.R + Rscript test-prediction-plot.R + +figure/test-correlation.pdf: data/combined-test-predictions.csv data/median-correlation.csv test-correlation-plot.R + Rscript test-correlation-plot.R + +# Validations + +validations: data/combined-cv.csv data/combined-test-predictions.csv + +data/combined-cv.csv: crossvalidation.rb data/combined.csv + ruby crossvalidation.rb combined.csv + +data/combined-test-predictions.csv: test-validation.rb data/test.csv data/combined.csv + ruby test-validation.rb combined.csv + +# Datasets + +datasets: data/median-correlation.csv data/test.csv data/combined.csv data/mazzatorta.csv data/swiss.csv data/test.json data/combined.json data/mazzatorta.json data/swiss.json + +# Medians for dataset correlation +data/median-correlation.csv: create-median-correlation.rb data/mazzatorta.csv data/swiss.csv + ruby create-median-correlation.rb + +# Test set +data/test.csv: create-test.rb data/mazzatorta.csv data/swiss.csv + ruby create-test.rb + +data/test.json: data/mazzatorta.json + cp data/mazzatorta.json data/test.json + +# Combined training set +data/combined.csv: create-combined.rb data/mazzatorta.csv data/swiss.csv + ruby create-combined.rb + +data/combined.json: data/mazzatorta.json + cp data/mazzatorta.json data/combined.json + +# Datasets with unique smiles +data/mazzatorta.csv: unique-smiles.rb data/LOAEL_mg_corrected_smiles_mmol.csv + ruby unique-smiles.rb data/LOAEL_mg_corrected_smiles_mmol.csv "mazzatorta" + +data/mazzatorta.json: data/LOAEL_mg_corrected_smiles_mmol.json + cp data/LOAEL_mg_corrected_smiles_mmol.json data/mazzatorta.json + +data/swiss.csv: unique-smiles.rb data/swissRat_chron_LOAEL_mmol.csv + ruby unique-smiles.rb data/swissRat_chron_LOAEL_mmol.csv "swiss" + +data/swiss.json: data/swissRat_chron_LOAEL_mmol.json + cp data/swissRat_chron_LOAEL_mmol.json data/swiss.json + +clean: + cd data && rm `ls -I "*LOAEL*" -I "*functional*" -I "*SMARTS*"` |