Changeset 2382

Timestamp:

Dec 21, 2010, 2:16:58 PM (12 years ago)

Author:

Peter

Message:

merged patch release 0.6.3 into trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• doc/Makefile.am (modified) (2 diffs)
• m4/version.m4 (modified) (1 diff)
• test/commandline.cc (modified) (1 diff)
• test/fisher.cc (modified) (3 diffs)
• yat/statistics/Fisher.cc (modified) (6 diffs)
• yat/utility/PCA.h (modified) (3 diffs)

trunk/NEWS

@@ -12 +12 @@
 
 yat 0.6.x series from http://dev.thep.lu.se/yat/svn/branches/0.6-stable
+
+Version 0.6.3 (released 21 December 2010)
+
+  - fixed overflow in statistics::Fisher (#638)
+  - fixed bug that double was hard-coded in function load<T>(6) (r2271)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.6.3
 
 Version 0.6.2 (released 18 May 2010)

trunk/doc/Makefile.am

@@ -6 +6 @@
 # Copyright (C) 2005 Peter Johansson
 # Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2009 Peter Johansson
+# Copyright (C) 2009, 2010 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -67 +67 @@
 
 $(DX_HTML_OUTPUT)/index.html: $(DOXYGEN_DEPS)
-  (cat doxygen.config && echo "INPUT = $(DOXYGEN_INPUT)" && \
+  @(cat doxygen.config && echo "INPUT = $(DOXYGEN_INPUT)" && \
   echo GENERATE_HTML = YES) | $(DOXYGEN) -;
-
 
 install-data-hook:

trunk/m4/version.m4

@@ -64 +64 @@
 # yat-0.6.1  3:1:0
 # yat-0.6.2  3:2:0
+# yat-0.6.3  3:3:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/commandline.cc

@@ -30 +30 @@
 
 #include <cassert>
+#include <cstdlib>
 #include <fstream>
 #include <stdexcept>

trunk/test/fisher.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2008, 2009 Peter Johansson
+  Copyright (C) 2008, 2009, 2010 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -24 +24 @@
 #include "yat/statistics/Fisher.h"
 
+#include <climits>
+
 using namespace theplu::yat;
 void test_p_value(test::Suite&);
 void test_p_value_approximative(test::Suite&);
 void test_p_value_exact(test::Suite&);
+void test_large_numbers(test::Suite&);
 
 int main(int argc, char* argv[])
@@ -65 +68 @@
   }
   test_p_value(suite);
+  test_large_numbers(suite);
   return suite.return_value();
+}
+
+
+void test_large_numbers(test::Suite& suite)
+{
+  // skip test if unsigned int is 16 bit
+  if ((UINT_MAX >> 16) == 0) {
+    suite.out() << "skipping test_large_numbers\n";
+    return;
+  }
+  
+  statistics::Fisher f;
+  double oddsratio = f.oddsratio(1166,63326825-1166,1095,66074759-1095);
+  if (oddsratio<0.5 || oddsratio>2) {
+    suite.err() << "oddsratio: " << oddsratio << "\n";
+    suite.err() << "expected ~ 1\n";
+    suite.xadd(false);
+  }
+  suite.add(suite.equal_fix(f.p_value(), 0.0123, 0.0001));
+  f.p_value_one_sided();
 }
 

trunk/yat/statistics/Fisher.cc

@@ -5 +5 @@
   Copyright (C) 2005 Peter Johansson
   Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009 Peter Johansson
+  Copyright (C) 2009, 2010 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -32 +32 @@
 
 #include <algorithm>
+#include <cassert>
 
 namespace theplu {
@@ -66 +67 @@
   void Fisher::expected(double& a, double& b, double& c, double& d) const
   {
-    double N = a_+b_+c_+d_;
-    a =((a_+b_)*(a_+c_)) / N;
-    b =((a_+b_)*(b_+d_)) / N;
-    c =((c_+d_)*(a_+c_)) / N;
-    d =((c_+d_)*(b_+d_)) / N;
+    // use floting point arithmetic to avoid overflow
+    double a1 = a_;
+    double b1 = b_;
+    double c1 = c_;
+    double d1 = d_;
+    double N = a1 + b1 + c1 + d1;
+    a =((a1+b1)*(a1+c1)) / N;
+    b =((a1+b1)*(b1+d1)) / N;
+    c =((c1+d1)*(a1+c1)) / N;
+    d =((c1+d1)*(b1+d1)) / N;
   }
 
@@ -100 +106 @@
     d_ = d;
 
-    oddsratio_=static_cast<double>(a*d)/static_cast<double>(b*c);
+    oddsratio_= (static_cast<double>(a) / static_cast<double>(b) * 
+                 static_cast<double>(d) / static_cast<double>(c) );
     return oddsratio_;
   }
@@ -120 +127 @@
       return p_value_approximative()/2.0;
     }
+    // check for overflow
+    assert(c_ <= c_+d_ && d_ <= c_+d_);
+    assert(a_ <= a_+b_ && b_ <= a_+b_);
+    assert(a_ <= a_+c_ && c_ <= a_+c_);
+
     return statistics::cdf_hypergeometric_P(c_, c_+d_, a_+b_, a_+c_);
   }
@@ -149 +161 @@
   }
 
-
 }}} // of namespace statistics, yat, and theplu

trunk/yat/utility/PCA.h

@@ -10 +10 @@
   Copyright (C) 2006 Jari Häkkinen
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
+  Copyright (C) 2010 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -43 +44 @@
      this space, all Nx1 vectors will have dimension Mx1. Hence
      the projection will have dimension MxM where each column is 
-     a point in the new space. Also, it assumes that M>N. The opposite
-     problem is added in the functions: process_transposed_problem and
-     projection_transposed()...
+     a point in the new space.
+
+     \note Currently number of rows, N, must be larger (or equal) than
+     number of columns, M.
   */
   class PCA
@@ -89 +91 @@
        3: Calculate eigenvalues according to \n 
           \f$ \lambda_{ii} = s_{ii}/N_{rows} \f$ \n
-       4: Sort eigenvectors (from matrix V) according to descending eigenvalues\n
     */
     void process(void);