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# Variables
datasets = data/median-correlation.csv data/test_log10.csv data/training_log10.csv data/mazzatorta_log10.csv data/swiss_log10.csv data/swiss_mg_dup.csv data/mazzatorta_mg_dup.csv data/all_mg_dup.csv
crossvalidations = data/training_log10-cv-0.csv data/training_log10-cv-1.csv data/training_log10-cv-2.csv
validations = data/training-test-predictions.csv $(crossvalidations) data/misclassifications.csv
figures = figures/functional-groups.pdf figures/test-prediction.pdf figures/prediction-test-correlation.pdf figures/dataset-variability.pdf figures/median-correlation.pdf figures/crossvalidation0.pdf figures/crossvalidation1.pdf figures/crossvalidation2.pdf
# Paper
loael.pdf: loael.tex
pdflatex loael.tex; pdflatex loael.tex
loael.tex: loael.md references.bibtex
pandoc -s --bibliography=references.bibtex --filter pandoc-crossref --filter pandoc-citeproc -o loael.tex loael.md
loael.md: loael.Rmd $(figures) $(datasets) $(validations)
export LANG=en_US.UTF-8; Rscript --vanilla -e "library(knitr); knit('loael.Rmd');"
loael.docx: loael.md
pandoc -s --bibliography=references.bibtex --latex-engine=pdflatex --filter pandoc-crossref --filter pandoc-citeproc -o loael.docx loael.md
loael.txt: loael.md
pandoc -s --bibliography=references.bibtex --latex-engine=pdflatex --filter pandoc-crossref --filter pandoc-citeproc -o loael.txt loael.md
# Figures
figures/functional-groups.pdf: data/functional-groups-reduced4R.csv
scripts/functional-groups.R
figures/dataset-variability.pdf: data/test_log10_database_fix.csv
scripts/dataset-variability.R
figures/crossvalidation0.pdf: data/training_log10-cv-0.csv
scripts/crossvalidation-plots.R 0
figures/crossvalidation1.pdf: data/training_log10-cv-1.csv
scripts/crossvalidation-plots.R 1
figures/crossvalidation2.pdf: data/training_log10-cv-2.csv
scripts/crossvalidation-plots.R 2
figures/test-prediction.pdf: data/predictions-measurements.csv
scripts/test-prediction-plot.R
figures/prediction-test-correlation.pdf: data/training-test-predictions.csv
scripts/prediction-test-correlation-plot.R
figures/median-correlation.pdf: data/median-correlation.csv
scripts/median-correlation-plot.R
# Validations
data/predictions-measurements.csv: data/training-test-predictions.csv data/test_log10.csv
scripts/test-prediction.rb
data/misclassifications.csv: data/training-test-predictions.csv
scripts/misclassifications.rb
data/training-test-predictions.csv: data/training-test-predictions.id
scripts/test-validation-results.rb
data/training-test-predictions.id: data/test_log10.csv data/training_log10.csv
scripts/testset-validation.rb
data/training_log10-cv-0.csv: data/training_log10-cv-0.id
scripts/crossvalidation-table.rb data/training_log10-cv-0.id
data/training_log10-cv-1.csv: data/training_log10-cv-1.id
scripts/crossvalidation-table.rb data/training_log10-cv-1.id
data/training_log10-cv-2.csv: data/training_log10-cv-2.id
scripts/crossvalidation-table.rb data/training_log10-cv-2.id
data/training_log10-cv-0.id: data/training_log10.csv
scripts/crossvalidation.rb training_log10.csv 0
data/training_log10-cv-1.id: data/training_log10.csv
scripts/crossvalidation.rb training_log10.csv 1
data/training_log10-cv-2.id: data/training_log10.csv
scripts/crossvalidation.rb training_log10.csv 2
# Datasets
# Functional groups
data/functional-groups-reduced4R.csv: data/functional-groups-reduced.csv
scripts/functional-groups4R.rb
# Medians for dataset correlation
data/median-correlation.csv: data/mazzatorta_log10.csv data/swiss_log10.csv
scripts/create-median-correlation.rb
# Test set
data/test_log10.csv: data/mazzatorta_log10.csv data/swiss_log10.csv
scripts/create-testset.rb
data/test_log10_database_fix.csv: data/test_log10.csv
sed 's/mazzatorta/Nestle/' data/test_log10.csv | sed 's/mazzatorta and swiss/Both/' | sed 's/swiss/FSVO/' > data/test_log10_database_fix.csv
# Training set
data/training_log10.csv: data/mazzatorta_log10.csv data/swiss_log10.csv
scripts/create-trainingset.rb
# -log10 transformations
data/mazzatorta_log10.csv: data/mazzatorta.csv
../lazar/scripts/mmol2-log10.rb data/mazzatorta.csv
sed -i 's/-log10(LOAEL)/LOAEL/' data/mazzatorta_log10.csv # R cannot parse -log10(LOAEL) header
data/swiss_log10.csv: data/swiss.csv
../lazar/scripts/mmol2-log10.rb data/swiss.csv
sed -i 's/-log10(LOAEL)/LOAEL/' data/swiss_log10.csv # R cannot parse -log10(LOAEL) header
# 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_mg_dup.csv: data/LOAEL_mg_corrected_smiles_mmol.csv
scripts/mazzatorta_mg_dup.rb data/LOAEL_mg_corrected_smiles_mmol.csv
data/swiss.csv: data/NOAEL-LOAEL_SMILES_rat_chron.csv
scripts/noael_loael2mmol.rb data/NOAEL-LOAEL_SMILES_rat_chron.csv
data/swiss_mg_dup.csv: data/NOAEL-LOAEL_SMILES_rat_chron.csv
scripts/noael_loael2swiss_mg_dup.rb data/NOAEL-LOAEL_SMILES_rat_chron.csv
data/all_mg_dup.csv: data/NOAEL-LOAEL_SMILES_rat_chron.csv data/LOAEL_mg_corrected_smiles_mmol.csv
scripts/all_mg_dup.rb
clean:
rm figures/*pdf
cd data && rm `ls -I "*LOAEL*" -I "*functional*" -I "*SMARTS*"`
mongo production --eval "db.dropDatabase()"
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