update

Author: Bill Majoros

DataFrame.py

@@ -28,6 +28,7 @@
 #   elem=df[i][j]
 #   df.toInt()
 #   df.toFloat()
+#   df.colToFloat(colIndex)
 #   header=df.getHeader()
 #   df.hashRowNames()
 #   df.hashColNames()
@@ -162,6 +163,9 @@ def __getitem__(self,i):
    def toInt(self):
       for row in self.matrix: row.toInt()
 
+   def colToFloat(self,colIndex):
+      for row in self.matrix: row[colIndex]=float(row[colIndex])
+
    def toFloat(self):
       for row in self.matrix: row.toFloat()
 

SummaryStats.py

@@ -31,6 +31,7 @@ def median(self,array):
         for x in array: a.append(x)
         a.sort()
         n=len(a)
+        if(n<1): raise Exception("median is undefined for 0 elements")
         halfN=int(n/2)
         if(n%2==1): return a[halfN]
         return (a[halfN-1]+a[halfN])/2

parse-stan.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+#=========================================================================
+# This is OPEN SOURCE SOFTWARE governed by the Gnu General Public
+# License (GPL) version 3, as described at www.opensource.org.
+# Author: William H. Majoros (bmajoros@alumni.duke.edu)
+#=========================================================================
+from __future__ import (absolute_import, division, print_function, 
+   unicode_literals, generators, nested_scopes, with_statement)
+from builtins import (bytes, dict, int, list, object, range, str, ascii,
+   chr, hex, input, next, oct, open, pow, round, super, filter, map, zip)
+# The above imports should allow this program to run in both Python 2 and
+# Python 3.  You might need to update your version of module "future".
+import sys
+import ProgramName
+from StanParser import StanParser
+
+#=========================================================================
+# main()
+#=========================================================================
+if(len(sys.argv)<3):
+    exit(ProgramName.get()+" <infile.txt> <var1> <var2> ...\n")
+infile=sys.argv[1]
+variables=sys.argv[2:]
+
+parser=StanParser(infile)
+#(median,mean,SD,min,max)=parser.getSummary(variable)
+#print("# posterior median=",median,sep="")
+samplesByVar=[]
+n=0
+for var in variables:
+    samples=parser.getVariable(var)
+    samplesByVar.append(samples)
+    n=len(samples)
+for i in range(n):
+    line=[]
+    for sample in samplesByVar: line.append(str(sample[i]))
+    print("\t".join(line))
+         
+
+

summarize-stan.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+#=========================================================================
+# This is OPEN SOURCE SOFTWARE governed by the Gnu General Public
+# License (GPL) version 3, as described at www.opensource.org.
+# Author: William H. Majoros (bmajoros@alumni.duke.edu)
+#=========================================================================
+from __future__ import (absolute_import, division, print_function, 
+   unicode_literals, generators, nested_scopes, with_statement)
+from builtins import (bytes, dict, int, list, object, range, str, ascii,
+   chr, hex, input, next, oct, open, pow, round, super, filter, map, zip)
+# The above imports should allow this program to run in both Python 2 and
+# Python 3.  You might need to update your version of module "future".
+import sys
+import ProgramName
+from StanParser import StanParser
+
+#=========================================================================
+# main()
+#=========================================================================
+if(len(sys.argv)<3):
+    exit(ProgramName.get()+" <infile.txt> <var1> <var2> ...\n")
+infile=sys.argv[1]
+variables=sys.argv[2:]
+
+parser=StanParser(infile)
+print("variable\tmedian\tSD")
+for var in variables:
+    (median,mean,SD,min,max)=parser.getSummary(var)
+    print(var,round(median,4),round(SD,5),sep="\t")
+
+