diff options
Diffstat (limited to 'r-util.rb')
| -rw-r--r-- | r-util.rb | 69 |
1 files changed, 54 insertions, 15 deletions
@@ -93,7 +93,7 @@ class RUtilTest < Test::Unit::TestCase def test_dataset_to_dataframe puts "dataset_to_dataframe" dataframe = @@rutil.dataset_to_dataframe(@@hamster,"NA",@@subjectid) - dataset_conv = @@rutil.dataframe_to_dataset(dataframe,@@subjectid) + dataset_conv = @@rutil.dataframe_to_dataset(dataframe,{},@@subjectid) dataset_conv_reloaded = OpenTox::Dataset.find(dataset_conv.uri,@@subjectid) @@resources << dataset_conv.uri dataset_equal(@@hamster,dataset_conv) @@ -101,7 +101,7 @@ class RUtilTest < Test::Unit::TestCase feats = @@hamster_features.features.keys[0..(@@hamster_features.features.keys.size/2)] dataframe = @@rutil.dataset_to_dataframe(@@hamster_features,"NA",@@subjectid,feats) - dataset_conv = @@rutil.dataframe_to_dataset(dataframe,@@subjectid) + dataset_conv = @@rutil.dataframe_to_dataset(dataframe,{},@@subjectid) dataset_conv_reloaded = OpenTox::Dataset.find(dataset_conv.uri,@@subjectid) @@resources << dataset_conv.uri [dataset_conv, dataset_conv_reloaded].each do |d| @@ -113,7 +113,7 @@ class RUtilTest < Test::Unit::TestCase assert d.data_entries[c]==nil || d.data_entries[c][f]==nil else assert_not_nil d.data_entries[c] - assert_equal @@hamster_features.data_entries[c][f],d.data_entries[c][f] + assert_equal @@hamster_features.data_entries[c][f].collect{|v|v.to_s},d.data_entries[c][f].collect{|v|v.to_s} end end end @@ -121,7 +121,7 @@ class RUtilTest < Test::Unit::TestCase dataframe = @@rutil.dataset_to_dataframe(@@hamster_features,"NA",@@subjectid) @@rutil.r.eval "#{dataframe} <- #{dataframe}[2:10,10:20]" - dataset_conv = @@rutil.dataframe_to_dataset(dataframe,@@subjectid) + dataset_conv = @@rutil.dataframe_to_dataset(dataframe,{},@@subjectid) dataset_conv_reloaded = OpenTox::Dataset.find(dataset_conv.uri,@@subjectid) @@resources << dataset_conv.uri [dataset_conv,dataset_conv_reloaded].each do |d| @@ -136,7 +136,7 @@ class RUtilTest < Test::Unit::TestCase assert d.data_entries[c]==nil || d.data_entries[c][f]==nil else assert_not_nil d.data_entries[c] - assert_equal @@hamster_features.data_entries[c][f],d.data_entries[c][f] + assert_equal @@hamster_features.data_entries[c][f].collect{|v|v.to_s},d.data_entries[c][f].collect{|v|v.to_s} end end end @@ -151,9 +151,9 @@ class RUtilTest < Test::Unit::TestCase # @@resources += [ res[0].uri, res[1].uri ] # @@strat = { :data => @@hamster, :split1 => res[0], :split2 => res[1] } data_combined = OpenTox::Dataset.merge(@@hamster,@@hamster_features,{},@@subjectid) - res = @@rutil.stratified_split(data_combined,0,@@split_ratio,@@subjectid,1) - @@resources += [ data_combined.uri, res[0].uri, res[1].uri ] - @@strat = {:data => data_combined, :split1 => res[0], :split2 => res[1] } + res1, res2 = @@rutil.stratified_split(data_combined,{},0,@@split_ratio,@@subjectid,1) + @@resources += [ data_combined.uri, res1.uri, res2.uri ] + @@strat = {:data => data_combined, :split1 => res1, :split2 => res2 } end @@strat end @@ -180,6 +180,45 @@ class RUtilTest < Test::Unit::TestCase end end end + + def test_k_fold_stratified_split + puts "test_k_fold_stratified_split" + data_combined = OpenTox::Dataset.merge(@@hamster,@@hamster_features,{},@@subjectid) + num_duplicates = 0 #hamster has no duplicates + num_folds = 10 + avg_split_size = (data_combined.compounds.size+num_duplicates)/num_folds.to_f + + @@resources += [ data_combined.uri ] + train, test = @@rutil.stratified_k_fold_split(data_combined,{},0,num_folds,@@subjectid,1) + @@resources += (train + test).collect{ |r| r.uri } + [train, test].each do |result| + assert result.is_a?(Array) + assert result.size==num_folds + end + sum_test = 0 + compounds_test = [] + num_folds.times do |i| + assert test[i].is_a?(OpenTox::Dataset) + assert test[i].compounds.size==avg_split_size.to_i || + test[i].compounds.size==(avg_split_size+1).to_i + sum_test+=test[i].compounds.size + compounds_test += test[i].compounds + + assert_equal (test[i].compounds.size+train[i].compounds.size),(data_combined.compounds.size+num_duplicates) + compounds = (test[i].compounds + train[i].compounds) + if num_duplicates==0 + assert_equal compounds.sort,data_combined.compounds.sort + else + assert_equal compounds.uniq.sort,data_combined.compounds.sort + end + end + assert_equal sum_test,(data_combined.compounds.size+num_duplicates) + if num_duplicates==0 + assert_equal compounds_test.sort,data_combined.compounds.sort + else + assert_equal compounds_test.uniq.sort,data_combined.compounds.sort + end + end def test_feature_value_plot puts "feature_value_plot" @@ -190,17 +229,17 @@ class RUtilTest < Test::Unit::TestCase @@resources += [dataset1.uri, dataset2.uri] files = [] #plot - [true,false].each do |fast_embedding| - next if fast_embedding==false and !@@rutil.package_installed?("smacof") - random_file = "/tmp/feature_value_plot_random_fast#{fast_embedding}.svg" - stratified_file = "/tmp/feature_value_plot_stratified_fast#{fast_embedding}.svg" + #[true,false].each do |fast_embedding| + # next if fast_embedding==false and !@@rutil.package_installed?("smacof") + random_file = "/tmp/feature_value_plot_random.svg" #_fast#{fast_embedding}.svg" + stratified_file = "/tmp/feature_value_plot_stratified.svg" #_fast#{fast_embedding}.svg" pre_files [random_file, stratified_file] @@rutil.feature_value_plot([random_file], dataset1.uri, dataset2.uri, - "first five", "rest", nil, fast_embedding, @@subjectid) + "first five", "rest", nil, @@subjectid) @@rutil.feature_value_plot([stratified_file], split[:split1].uri, split[:split2].uri, - "five percent stratified", "rest", nil, fast_embedding, @@subjectid) + "five percent stratified", "rest", nil, @@subjectid) files += [random_file, stratified_file] - end + #end #cleanup post_files files end |