rf models, similarity 0.1

1 files changed, 16 insertions, 13 deletions

diff --git a/Makefile b/Makefile
index 85b8518..574325e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 # Variables
 
-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
+datasets = data/median-correlation.csv data/test_log10.csv data/training_log10.csv data/mazzatorta_log10.csv data/swiss_log10.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/test-correlation.pdf figures/crossvalidation.pdf figures/dataset-variability.pdf
@@ -21,7 +21,7 @@ loael.docx: loael.md
 figures/functional-groups.pdf: data/functional-groups-reduced4R.csv
 	scripts/functional-groups.R
 
-figures/dataset-variability.pdf: data/mazzatorta.csv data/swiss.csv
+figures/dataset-variability.pdf: data/mazzatorta_log10.csv data/swiss_log10.csv
 	scripts/dataset-variability.R
 
 figures/crossvalidation.pdf: $(crossvalidations)
@@ -39,10 +39,10 @@ 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.csv
+	scripts/test-validation-results.rb 
 
 data/training-test-predictions.id: data/test_log10.csv data/training_log10.csv
-	scripts/test-validation.rb > data/training-test-predictions.id
+	scripts/test-validation.rb
 
 data/training_log10-cv-0.csv: data/training_log10.csv
 	scripts/crossvalidation.rb training_log10.csv 0
@@ -60,36 +60,39 @@ data/functional-groups-reduced4R.csv: data/functional-groups-reduced.csv
 
 # Medians for dataset correlation
 data/median-correlation.csv: data/mazzatorta_log10.csv data/swiss_log10.csv
-	scripts/create-median-correlation.rb > data/median-correlation.csv
+	scripts/create-median-correlation.rb
 
 # Test set
 data/test_log10.csv: data/mazzatorta_log10.csv data/swiss_log10.csv
-	scripts/create-test.rb > data/test_log10.csv
+	scripts/create-test.rb 
 
-data/test.json: data/mazzatorta.json 
-	cp data/mazzatorta.json data/test.json
+#data/test.json: data/mazzatorta.json 
+	#cp data/mazzatorta.json data/test.json
 
 # Combined training set
 data/training_log10.csv: data/mazzatorta_log10.csv data/swiss_log10.csv
-	scripts/create-training.rb > data/training_log10.csv
+	scripts/create-training.rb
 
-data/training.json: data/mazzatorta.json 
-	cp data/mazzatorta.json data/training.json
+#data/training.json: data/mazzatorta.json 
+	#cp data/mazzatorta.json data/training.json
 
 # -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.csv
+	scripts/mazzatorta-unique-smiles.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.csv
+	scripts/noael_loael2mmol.rb data/NOAEL-LOAEL_SMILES_rat_chron.csv
 
 clean:
 	rm figures/*pdf
 	cd data && rm `ls -I "*LOAEL*" -I "*functional*" -I "*SMARTS*"`
+	mongo development --eval "db.dropDatabase()"