p-value caluculation script

1 files changed, 60 insertions, 0 deletions

diff --git a/pvalue.py b/pvalue.py
new file mode 100755
index 0000000..15c6e10
--- /dev/null
+++ b/pvalue.py
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+#!/usr/bin/env python
+
+import os
+import sys
+
+import math
+import numpy
+
+import data
+
+# Haversine distance calculation
+# --------- -------- -----------
+
+rearth = 6371.
+deg2rad = 3.141592653589793 / 180.
+
+def hdist(a, b):
+    lat1 = a[:, 0] * deg2rad
+    lon1 = a[:, 1] * deg2rad
+    lat2 = b[:, 0] * deg2rad
+    lon2 = b[:, 1] * deg2rad
+
+    dlat = abs(lat1-lat2)
+    dlon = abs(lon1-lon2)
+
+    al = numpy.sin(dlat/2)**2  + numpy.cos(lat1) * numpy.cos(lat2) * (numpy.sin(dlon/2)**2)
+    d = numpy.arctan2(numpy.sqrt(al), numpy.sqrt(1.-al))
+
+    hd = 2. * rearth * d
+
+    return hd
+
+
+# Read the inputs
+# ---- --- ------
+
+def readcsv(f):
+    return numpy.genfromtxt(f, delimiter=',', skip_header=1)[:, 1:3]
+
+answer = readcsv(os.path.join(data.path, 'test_answer.csv'))
+
+tables = [readcsv(f) for f in sys.argv if '.csv' in f]
+etables = [hdist(t, answer) for t in tables]
+
+# Calculate p-values
+# --------- --------
+
+pvalue = numpy.zeros((len(tables), len(tables)))
+
+for i, a in enumerate(etables):
+    for j, b in enumerate(etables):
+        if i == j:
+            continue
+        d = b - a
+        var = (numpy.mean((a - numpy.mean(a))**2)
+                + numpy.mean((b - numpy.mean(b))**2)) / 2.
+        pv = 1 - .5 * (1 + math.erf(numpy.mean(d) / numpy.sqrt(2 * var)))
+        pvalue[i, j] = pv
+
+print pvalue