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

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.h (modified) (11 diffs)

trunk/yat/statistics/Fisher.h

@@ -1 +1 @@
 #ifndef _theplu_yat_statistics_fisher_
-#define _theplu_yat_statistics_fisher_ 
+#define _theplu_yat_statistics_fisher_
 
 // $Id$
@@ -7 +7 @@
   Copyright (C) 2004, 2005 Peter Johansson
   Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2011 Peter Johansson
+  Copyright (C) 2009, 2011, 2013 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -25 +25 @@
 */
 
+#include <yat/utility/deprecate.h>
+
 namespace theplu {
 namespace yat {
-namespace statistics {  
+namespace statistics {
+
   /**
-     @brief Fisher's exact test.   
+     @brief Fisher's exact test.
 
      Fisher's Exact test is a procedure that you can use for data
@@ -52 +55 @@
      because a large sample approximation (that the Chi-square test
      relies on) is very reasonable. If all elements are larger than
-     10 a Chi-square test is reasonable to use. 
-     
+     10 a Chi-square test is reasonable to use.
+
      @note The statistica assumes that each column and row sum,
      respectively, are fixed. Just because you have a 2x2 table, this
@@ -59 +62 @@
      e.g. Barnard's test for alternative.
   */
-  
+
   class Fisher
   {
-  
+
   public:
     ///
@@ -70 +73 @@
 
     ///
-    /// Destructor 
+    /// Destructor
     ///
     virtual ~Fisher(void);
-         
-    
+
+
     /**
        The Chi2 score is calculated as \f$ \sum
        \frac{(O_i-E_i)^2}{E_i}\f$ where \a E is expected value and \a
        O is observed value.
+
+       \see expected(double&, double&, double&, double&)
 
        \return Chi2 score
@@ -110 +115 @@
 
     /**
+       Calculates probability to get oddsratio (or smaller).
+
        If all elements in table is at least minimum_size(), a Chi2
        approximation is used.
-       
+
+       \since New in yat 0.11
+     */
+    double p_left(void) const;
+
+    /**
+       Calculates probability to get oddsratio (or greater).
+
+       If all elements in table is at least minimum_size(), a Chi2
+       approximation is used.
+
+       \since New in yat 0.11
+     */
+    double p_right(void) const;
+
+    /**
+       If all elements in table is at least minimum_size(), a Chi2
+       approximation is used.
+
        Otherwise a two-sided p-value is calculated using the
        hypergeometric distribution
@@ -120 +145 @@
        \return two-sided p-value
     */
-    double p_value() const;
-    
+    double p_value(void) const;
+
     ///
     /// One-sided p-value is probability to get larger (or equal) oddsratio.
@@ -130 +155 @@
     /// @return One-sided p-value
     ///
-    double p_value_one_sided() const;
-    
-    /**
-       Function calculating odds ratio from 2x2 table 
+    /// \deprecated Provided for backward compatibility with the 0.10
+    /// API. Use p_right() instead.
+    ///
+    double p_value_one_sided() const YAT_DEPRECATE;
+
+    /**
+       Function calculating odds ratio from 2x2 table
        \f[ \begin{tabular}{|c|c|}
        \hline a&b \tabularnewline \hline c&d \tabularnewline \hline
@@ -140 +168 @@
        Object will remember the values of \a a, \a b, \a c, and \a d.
 
-       @return odds ratio. 
+       @return odds ratio.
 
        @throw If table is invalid a runtime_error is thrown. A table
        is invalid if a row or column sum is zero.
     */
-    double oddsratio(const unsigned int a, const unsigned int b, 
+    double oddsratio(const unsigned int a, const unsigned int b,
                      const unsigned int c, const unsigned int d);
 
@@ -156 +184 @@
 
   private:
-    bool calculate_p_exact() const;
+    bool calculate_p_exact(void) const;
 
     // two-sided
     double p_value_approximative(void) const;
+    double p_left_exact(void) const;
+    double p_right_exact(void) const;
     //two-sided
     double p_value_exact(void) const;