erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / cisstat / chi2.py

diff --git a/cistematic/cisstat/chi2.py b/cistematic/cisstat/chi2.py
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+###########################################################################
+#                                                                         #
+# C O P Y R I G H T   N O T I C E                                         #
+#  Copyright (c) 2003-10 by:                                              #
+#    * California Institute of Technology                                 #
+#                                                                         #
+#    All Rights Reserved.                                                 #
+#                                                                         #
+# Permission is hereby granted, free of charge, to any person             #
+# obtaining a copy of this software and associated documentation files    #
+# (the "Software"), to deal in the Software without restriction,          #
+# including without limitation the rights to use, copy, modify, merge,    #
+# publish, distribute, sublicense, and/or sell copies of the Software,    #
+# and to permit persons to whom the Software is furnished to do so,       #
+# subject to the following conditions:                                    #
+#                                                                         #
+# The above copyright notice and this permission notice shall be          #
+# included in all copies or substantial portions of the Software.         #
+#                                                                         #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
+# SOFTWARE.                                                               #
+###########################################################################
+#
+#
+
+def chiSquare(A, B, C, D):
+    """ Chi-square for a 2x2 table, as described in Gopal Kanji's 100 Statistical Tests
+        note that we only have one degree of freedom, work best if no cell is less than 3.
+        Table has form:
+                                A   |    B      | A + B
+                            -----------------------------
+                                C   |    D      | C + D
+                            -----------------------------
+                            A + C | B + D   | A + B + C + D
+    """
+    chiAB = long(A + B)
+    chiCD = long(C +D)
+    chiAC = long(A + C)
+    chiBD = long(B + D)
+    chiAD = long(A * D)
+    chiBC = long(B * C)
+    chiN = long(chiAB + chiCD)
+    
+    chiNum = long(chiN - 1) * long(pow(chiAD - chiBC, 2)) 
+    chiDen = long(chiAB * chiAC * chiBD * chiCD)
+
+    return long(chiNum / chiDen)
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