diff options
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 83 |
1 files changed, 42 insertions, 41 deletions
@@ -1,9 +1,9 @@ # Variables -datasets = data/median-correlation.csv data/test.csv data/training.csv data/mazzatorta.csv data/swiss.csv data/test.json data/training.json data/mazzatorta.json data/swiss.json +datasets = data/median-correlation.csv data/test_log10.csv data/training_log10.csv data/mazzatorta_log10.csv data/swiss_log10.csv data/test.json data/training.json data/mazzatorta.json data/swiss.json crossvalidations = data/training-cv-0.csv data/training-cv-1.csv data/training-cv-2.csv validations = data/training-test-predictions.csv $(crossvalidations) data/misclassifications.csv -figures = figure/functional-groups.pdf figure/test-prediction.pdf figure/test-correlation.pdf figure/crossvalidation.pdf figure/dataset-variability.pdf +figures = figures/functional-groups.pdf figures/test-prediction.pdf figures/test-correlation.pdf figures/crossvalidation.pdf figures/dataset-variability.pdf # Paper @@ -11,81 +11,82 @@ 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) $(datasets) $(validations) - Rscript --vanilla -e "library(knitr); knit('loael.Rmd');" + scripts/--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 -figure/functional-groups.pdf: data/functional-groups-reduced4R.csv functional-groups.R - Rscript functional-groups.R +figures/functional-groups.pdf: data/functional-groups-reduced4R.csv + scripts/functional-groups.R -figure/dataset-variability.pdf: data/mazzatorta.csv data/swiss.csv dataset-variability.R - Rscript dataset-variability.R +figures/dataset-variability.pdf: data/mazzatorta.csv data/swiss.csv + scripts/dataset-variability.R -figure/crossvalidation.pdf: $(crossvalidations) - Rscript crossvalidation-plots.R +figures/crossvalidation.pdf: $(crossvalidations) + scripts/crossvalidation-plots.R -figure/test-prediction.pdf: data/training-test-predictions.csv data/median-correlation.csv test-prediction-plot.R - Rscript test-prediction-plot.R +figures/test-prediction.pdf: data/training-test-predictions.csv data/median-correlation.csv + scripts/test-prediction-plot.R -figure/test-correlation.pdf: data/training-test-predictions.csv data/median-correlation.csv test-correlation-plot.R - Rscript test-correlation-plot.R +figures/test-correlation.pdf: data/training-test-predictions.csv data/median-correlation.csv + scripts/test-correlation-plot.R # Validations -data/misclassifications.csv: misclassifications.rb data/training-test-predictions.csv - ruby misclassifications.rb +data/misclassifications.csv: data/training-test-predictions.csv + scripts/misclassifications.rb -data/training-test-predictions.csv: test-validation.rb data/test.csv data/training.csv - ruby test-validation.rb training.csv +data/training-test-predictions.csv: data/test_log10.csv data/training_log10.csv + scripts/test-validation.rb training.csv -data/training-cv-0.csv: crossvalidation.rb data/training.csv - ruby crossvalidation.rb training.csv 0 +data/training-cv-0.csv: data/training_log10.csv + scripts/crossvalidation.rb training.csv 0 -data/training-cv-1.csv: crossvalidation.rb data/training.csv - ruby crossvalidation.rb training.csv 1 +data/training-cv-1.csv: data/training_log10.csv + scripts/crossvalidation.rb training.csv 1 -data/training-cv-2.csv: crossvalidation.rb data/training.csv - ruby crossvalidation.rb training.csv 2 +data/training-cv-2.csv: data/training_log10.csv + scripts/crossvalidation.rb training.csv 2 # Datasets -data/functional-groups-reduced4R.csv: data/functional-groups-reduced.csv functional-groups4R.rb - ruby functional-groups4R.rb +data/functional-groups-reduced4R.csv: data/functional-groups-reduced.csv + scripts/functional-groups4R.rb # Medians for dataset correlation -data/median-correlation.csv: create-median-correlation.rb data/mazzatorta.csv data/swiss.csv - ruby create-median-correlation.rb +data/median-correlation.csv: data/mazzatorta.csv data/swiss.csv + scripts/create-median-correlation.rb # Test set -data/test.csv: create-test.rb data/mazzatorta.csv data/swiss.csv - ruby create-test.rb +data/test_log10.csv: data/mazzatorta_log10.csv data/swiss_log10.csv + scripts/create-test.rb data/test.json: data/mazzatorta.json cp data/mazzatorta.json data/test.json # Combined training set -data/training.csv: create-training.rb data/mazzatorta.csv data/swiss.csv - ruby create-training.rb +data/training_log10.csv: data/mazzatorta_log10.csv data/swiss_log10.csv + scripts/create-training.rb data/training.json: data/mazzatorta.json cp data/mazzatorta.json data/training.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" +# -log10 transformations +data/mazzatorta_log10.csv: data/mazzatorta.csv + ../lazar/scripts/mmol2-log10.rb data/mazzatorta.csv -data/mazzatorta.json: data/LOAEL_mg_corrected_smiles_mmol.json - cp data/LOAEL_mg_corrected_smiles_mmol.json data/mazzatorta.json +data/swiss_log10.csv: data/swiss.csv + ../lazar/scripts/mmol2-log10.rb data/swiss.csv -data/swiss.csv: unique-smiles.rb data/swissRat_chron_LOAEL_mmol.csv - ruby unique-smiles.rb data/swissRat_chron_LOAEL_mmol.csv "swiss" +# Datasets with unique smiles +data/mazzatorta.csv: data/LOAEL_mg_corrected_smiles_mmol.csv + scripts/mazzatorta-unique-smiles.rb data/LOAEL_mg_corrected_smiles_mmol.csv > data/mazzatorta.csv -data/swiss.json: data/swissRat_chron_LOAEL_mmol.json - cp data/swissRat_chron_LOAEL_mmol.json data/swiss.json +data/swiss.csv: data/NOAEL-LOAEL_SMILES_rat_chron.csv + scripts/noael_loael2mmol.rb data/NOAEL-LOAEL_SMILES_rat_chron.csv > data/swiss.csv clean: - rm figure/*pdf + rm figures/*pdf cd data && rm `ls -I "*LOAEL*" -I "*functional*" -I "*SMARTS*"` |