Changeset 779 for trunk/test

Timestamp:

Mar 5, 2007, 7:58:30 PM (16 years ago)

Author:

Peter

Message:

Refs #101

Location:

trunk/test

Files:

• Makefile.am (modified) (3 diffs)
• consensus_inputranker_test.cc (modified) (2 diffs)
• feature_selection_test.cc (modified) (2 diffs)
• inputranker_test.cc (modified) (2 diffs)
• roc_test.cc (added)
• score_test.cc (modified) (5 diffs)
• subset_generator_test.cc (modified) (3 diffs)

trunk/test/Makefile.am

@@ -7 +7 @@
 # Copyright (C) 2005 Jari Häkkinen, Peter Johansson
 # Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
+# Copyright (C) 2007 Peter Johansson
 #
 # This file is part of the yat library, http://lev.thep.lu.se/trac/yat
@@ -29 +30 @@
   ensemble_test feature_selection_test fileutil_test inputranker_test \
   kernel_test kernel_lookup_test matrix_test matrix_lookup_test       \
-  ncc_test nni_test pca_test regression_test rnd_test score_test      \
+  ncc_test nni_test pca_test regression_test rnd_test roc_test \
+  score_test      \
   statistics_test subset_generator_test svd_test svm_test target_test \
   utility_test vector_test
@@ -60 +62 @@
 regression_test_SOURCES = regression_test.cc
 rnd_test_SOURCES = rnd_test.cc
+roc_test_SOURCES = roc_test.cc
 score_test_SOURCES = score_test.cc
 statistics_test_SOURCES = statistics_test.cc

trunk/test/consensus_inputranker_test.cc

@@ -23 +23 @@
 
 #include "yat/classifier/ConsensusInputRanker.h"
-#include "yat/statistics/ROC.h"
+#include "yat/statistics/ROCscore.h"
 #include "yat/utility/matrix.h"
 #include "yat/classifier/MatrixLookup.h"
@@ -59 +59 @@
 
   
-  theplu::yat::statistics::ROC roc;
+  theplu::yat::statistics::ROCscore roc;
   theplu::yat::classifier::CrossValidationSampler sampler(target,30,3);
   *error << "Building Consensus_Inputranker" << std::endl;

trunk/test/feature_selection_test.cc

@@ -24 +24 @@
 #include "yat/classifier/FeatureSelectorIR.h"
 #include "yat/classifier/FeatureSelectorRandom.h"
-#include "yat/statistics/ROC.h"
+#include "yat/statistics/ROCscore.h"
 
 #include <fstream>
@@ -45 +45 @@
   bool ok = true;
 
-  statistics::ROC roc;
+  statistics::ROCscore roc;
   classifier::FeatureSelectorIR f(roc, 12);
   classifier::FeatureSelectorRandom f2(12);

trunk/test/inputranker_test.cc

@@ -23 +23 @@
 
 #include "yat/classifier/InputRanker.h"
-#include "yat/statistics/ROC.h"
+#include "yat/statistics/ROCscore.h"
 #include "yat/utility/matrix.h"
 #include "yat/classifier/MatrixLookup.h"
@@ -57 +57 @@
   is.close();
 
-  statistics::ROC roc;
+  statistics::ROCscore roc;
   classifier::InputRanker ir(data,target,roc);
   if (ir.id()[0]!=2 || ir.id()[1]!=0 || ir.id()[2]!=1){

trunk/test/score_test.cc

@@ -25 +25 @@
 #include "yat/statistics/FoldChange.h"
 #include "yat/statistics/Pearson.h"
-#include "yat/statistics/ROC.h"
-#include "yat/statistics/SAM.h"
+#include "yat/statistics/ROCscore.h"
+#include "yat/statistics/SAMScore.h"
 #include "yat/statistics/tScore.h"
 #include "yat/statistics/WilcoxonFoldChange.h"
@@ -52 +52 @@
   bool ok = true;
 
-  *error << "testing ROC" << std::endl;
+  *error << "testing ROCscore" << std::endl;
   utility::vector value(31);
   std::vector<std::string> label(31,"negative");
@@ -60 +60 @@
   for (size_t i=0; i<value.size(); i++) 
     value(i)=i;
-  statistics::ROC roc;
+  statistics::ROCscore roc;
   double area = roc.score(target, value);
   if (area!=1.0){
@@ -73 +73 @@
     *error << "test_roc: area is " << area << " should be 1.0" 
            << std::endl;
-    ok = false;
-  }
-  
-  double p = roc.p_value();
-  double p_matlab = 0.00000115;
-  if (p/p_matlab > 1.01 | p/p_matlab < 0.99){
-    *error << "get_p_approx: p-value not correct" << std::endl;
-    ok = false;
-  }
-  roc.minimum_size() = 20;
-  p = roc.p_value();
-  if (p > pow(10, -8.0) | p < pow(10, -9.0)){
-    *error << "get_p_exact: p-value not correct" << std::endl;
     ok = false;
   }
@@ -141 +128 @@
   statistics::WilcoxonFoldChange wfc(true);
 
-  *error << "testing SAM" << std::endl;
-  statistics::SAM sam(1.0,true);
+  *error << "testing SAMScore" << std::endl;
+  statistics::SAMScore sam(1.0,true);
 
 

trunk/test/subset_generator_test.cc

@@ -32 +32 @@
 #include "yat/classifier/SVM.h"
 #include "yat/classifier/NCC.h"
-#include "yat/statistics/ROC.h"
+#include "yat/statistics/ROCscore.h"
 #include "yat/statistics/PearsonDistance.h"
 #include "yat/utility/matrix.h"
@@ -78 +78 @@
   classifier::CrossValidationSampler sampler(target, 30, 3);
 
-  statistics::ROC score;
+  statistics::ROCscore score;
   classifier::FeatureSelectorIR fs(score, 96, 0);
   *error << "building SubsetGenerator" << std::endl;
@@ -96 +96 @@
   for (size_t i = 0; i<out.size(); ++i)
     out(i)=ensemble_svm.validate()[0][i].mean();
-  statistics::ROC roc;
+  statistics::ROCscore roc;
   *error << roc.score(target,out) << std::endl;