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# 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) $(datasets) $(validations)
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
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: $(crossvalidations)
Rscript 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
figure/test-correlation.pdf: data/training-test-predictions.csv data/median-correlation.csv test-correlation-plot.R
Rscript test-correlation-plot.R
# Validations
data/training-test-predictions.csv: test-validation.rb data/test.csv data/training.csv
ruby test-validation.rb training.csv
data/training-cv-0.csv: crossvalidation.rb data/training.csv
ruby crossvalidation.rb training.csv 0
data/training-cv-1.csv: crossvalidation.rb data/training.csv
ruby crossvalidation.rb training.csv 1
data/training-cv-2.csv: crossvalidation.rb data/training.csv
ruby crossvalidation.rb training.csv 2
# Datasets
data/functional-groups-reduced4R.csv: data/functional-groups-reduced.csv functional-groups4R.rb
ruby 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
# 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/training.csv: create-training.rb data/mazzatorta.csv data/swiss.csv
ruby 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"
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:
rm figure/*pdf
cd data && rm `ls -I "*LOAEL*" -I "*functional*" -I "*SMARTS*"`
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