From 74ee6242ea65e88074c2b1df85c0f4428b79333b Mon Sep 17 00:00:00 2001
From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Wed, 16 May 2012 13:52:24 -0400
Subject: [PATCH] replaced p-value with zscore for lookup in ztable.
---
cooccurrencecommand.cpp | 14 +++++++++++---
trialSwap2.cpp | 36 ++++++++++++++++++++----------------
2 files changed, 31 insertions(+), 19 deletions(-)
diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index 75b87fa..6363f2a 100644
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -180,7 +180,7 @@ int CooccurrenceCommand::execute(){
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
- out << "metric\tlabel\tScore\tpValue\n";
+ out << "metric\tlabel\tScore\tzScore\n";
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -530,12 +530,20 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
m->mothurOutEndLine(); m->mothurOut("average metric score: " + toString(nullMean)); m->mothurOutEndLine();
+ //calc_p_value is not a statistical p-value, it's just the average that are either > or < the initscore.
+ //All it does is show what is expected in a competitively structured community
+ //zscore is output so p-value can be looked up in a ztable
double pvalue = 0.0;
if (metric == "cscore" || metric == "checker") { pvalue = trial.calc_pvalue_greaterthan (stats, initscore); }
else{ pvalue = trial.calc_pvalue_lessthan (stats, initscore); }
+
+ double sd = trial.getSD(runs, stats, nullMean);
+
+ double zscore = trial.get_zscore(sd, nullMean, initscore);
- m->mothurOut("pvalue: " + toString(pvalue)); m->mothurOutEndLine();
- out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << pvalue << endl;
+ m->mothurOut("zscore: " + toString(zscore)); m->mothurOutEndLine();
+ m->mothurOut("standard deviation: " + toString(sd)); m->mothurOutEndLine();
+ out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << endl;
return 0;
}
diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index 1524890..71c3027 100644
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -293,26 +293,30 @@ double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vecto
/**************************************************************************************************/
double TrialSwap2::getSD (int runs, vector<double> scorevec, double nullMean)
{
- double sum = 0;
- for(int i=0;i<runs;i++)
- {
- if (m->control_pressed) { return 0; }
- sum += pow((scorevec[i] - nullMean),2);
- }
- return sqrt( (1/runs) * sum );
+ try{
+ double sum = 0;
+ for(int i=0;i<runs;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ sum += pow((scorevec[i] - nullMean),2);
+ }
+ return sqrt( (1/double(runs)) * sum );
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "getSD");
+ exit(1);
+ }
}
/**************************************************************************************************/
double TrialSwap2::get_zscore (double sd, double nullMean, double initscore)
{
- map<double, double> ztable;
-
- ztable["0.00"] = 0.5;
-
- double z;
-
- z = (initscore - nullMean) / sd;
-
- return z;
+ try {
+ return (initscore - nullMean) / sd;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "get_zscore");
+ exit(1);
+ }
}
/**************************************************************************************************/
int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
--
2.39.5