diff options
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 42 |
1 files changed, 25 insertions, 17 deletions
@@ -1,9 +1,16 @@ +# 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 +crossvalidations = data/training-cv-0.csv data/training-cv-1.csv data/training-cv-2.csv +validations = data/training-test-predictions.csv $(crossvalidations) +figures = figure/functional-groups.pdf figure/test-prediction.pdf figure/test-correlation.pdf figure/crossvalidation.pdf figure/dataset-variability.pdf + # 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 +loael.md: loael.Rmd $(figures) $(datasets) $(validations) Rscript --vanilla -e "library(knitr); knit('loael.Rmd');" loael.docx: loael.md @@ -11,36 +18,36 @@ loael.docx: loael.md # 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 +figure/crossvalidation.pdf: $(crossvalidations) Rscript crossvalidation-plots.R -figure/test-prediction.pdf: data/combined-test-predictions.csv data/median-correlation.csv test-prediction-plot.R +figure/test-prediction.pdf: data/training-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 +figure/test-correlation.pdf: data/training-test-predictions.csv data/median-correlation.csv test-correlation-plot.R Rscript test-correlation-plot.R # Validations -validations: data/combined-test-predictions.csv data/combined-cv.csv +data/training-test-predictions.csv: test-validation.rb data/test.csv data/training.csv + ruby test-validation.rb training.csv -data/combined-test-predictions.csv: test-validation.rb data/test.csv data/combined.csv - ruby test-validation.rb combined.csv +data/training-cv-0.csv: crossvalidation.rb data/training.csv + ruby crossvalidation.rb training.csv 0 -data/combined-cv.csv: crossvalidation.rb data/combined.csv - ruby crossvalidation.rb combined.csv +data/training-cv-1.csv: crossvalidation.rb data/training.csv + ruby crossvalidation.rb training.csv 1 -# Datasets +data/training-cv-2.csv: crossvalidation.rb data/training.csv + ruby crossvalidation.rb training.csv 2 -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 +# Datasets data/functional-groups-reduced4R.csv: data/functional-groups-reduced.csv functional-groups4R.rb ruby functional-groups4R.rb @@ -57,11 +64,11 @@ 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/training.csv: create-training.rb data/mazzatorta.csv data/swiss.csv + ruby create-training.rb -data/combined.json: data/mazzatorta.json - cp data/mazzatorta.json data/combined.json +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 @@ -77,4 +84,5 @@ data/swiss.json: data/swissRat_chron_LOAEL_mmol.json cp data/swissRat_chron_LOAEL_mmol.json data/swiss.json clean: + rm figure/*pdf cd data && rm `ls -I "*LOAEL*" -I "*functional*" -I "*SMARTS*"` |