Changeset 3004 for trunk/yat/statistics/Fisher.cc

Timestamp:

Mar 24, 2013, 1:51:14 AM (10 years ago)

Author:

Peter

Message:

refs #689. Deprecate Fisher::one_sided_p; implement Fisher::left_p and right_p.

File:

• trunk/yat/statistics/Fisher.cc (modified) (8 diffs)

trunk/yat/statistics/Fisher.cc

@@ -5 +5 @@
   Copyright (C) 2005 Peter Johansson
   Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
+  Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -40 +40 @@
 namespace statistics {
 
-  
+
   Fisher::Fisher()
     : a_(0), b_(0), c_(0), d_(0), minimum_size_(10), oddsratio_(1.0)
@@ -54 +54 @@
   bool Fisher::calculate_p_exact(void) const
   {
-    return ( a_<minimum_size_ || b_<minimum_size_ || 
-             c_<minimum_size_ || d_<minimum_size_); 
-  }
-
-  double Fisher::Chi2() const
+    return ( a_<minimum_size_ || b_<minimum_size_ ||
+             c_<minimum_size_ || d_<minimum_size_);
+  }
+
+  double Fisher::Chi2(void) const
   {
     double a,b,c,d;
     expected(a,b,c,d);
-    return (a-a_)*(a-a_)/a + (b-b_)*(b-b_)/b + 
+    return (a-a_)*(a-a_)/a + (b-b_)*(b-b_)/b +
       (c-c_)*(c-c_)/c + (d-d_)*(d-d_)/d;
   }
@@ -97 +97 @@
                            const unsigned int b,
                            const unsigned int c,
-                           const unsigned int d) 
+                           const unsigned int d)
   {
     // If a column sum or a row sum is zero, the table is nonsense
@@ -108 +108 @@
     d_ = d;
 
-    oddsratio_= (static_cast<double>(a) / static_cast<double>(b) * 
+    oddsratio_= (static_cast<double>(a) / static_cast<double>(b) *
                  static_cast<double>(d) / static_cast<double>(c) );
     return oddsratio_;
@@ -120 +120 @@
 
 
-  double Fisher::p_value() const
+  double Fisher::p_left(void) const
+  {
+    if (!calculate_p_exact()) {
+      if (oddsratio_>1.0)
+        return 1.0-p_value_approximative()/2.0;
+      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 cdf_hypergeometric_P(a_, a_+b_, c_+d_, a_+c_);
+  }
+
+
+  double Fisher::p_value(void) const
   {
     if (calculate_p_exact())
@@ -128 +144 @@
 
 
-  double Fisher::p_value_one_sided() const
+  double Fisher::p_right(void) const
   {
     if (!calculate_p_exact()) {
@@ -140 +156 @@
     assert(a_ <= a_+c_ && c_ <= a_+c_);
 
-    return statistics::cdf_hypergeometric_P(c_, c_+d_, a_+b_, a_+c_);
-  }
-
-
-  double Fisher::p_value_approximative() const
+    return cdf_hypergeometric_P(c_, c_+d_, a_+b_, a_+c_);
+  }
+
+
+  double Fisher::p_value_one_sided(void) const
+  {
+    return p_right();
+  }
+
+
+  double Fisher::p_value_approximative(void) const
   {
     return gsl_cdf_chisq_Q(Chi2(), 1.0);
   }
 
-  double Fisher::p_value_exact() const
-  { 
+
+  double Fisher::p_left_exact(void) const
+  {
+    return 0;
+  }
+
+
+  double Fisher::p_right_exact(void) const
+  {
+    return 0;
+  }
+
+
+  double Fisher::p_value_exact(void) const
+  {
     double res=0;
     double a, c, tmp;
     expected(a, tmp, c, tmp);
-    // sum P(x) over x for which abs(x-E(a))>=abs(a-E(a))  
+    // sum P(x) over x for which abs(x-E(a))>=abs(a-E(a))
 
     // counting left tail