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# 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*"`
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