verified this still works with new funcs

Author: ito-takuya

testCode/compareMatlabFunctions.m

@@ -0,0 +1,61 @@
+% Taku Ito
+% 6/16/2017
+
+% Test script to test code for permutation testing in matlab
+clear all
+clc
+
+addpath('../matlabCode/')
+addpath('../matlabCode/mult_comp_perm_t1/')
+
+permutations=10000;
+
+%% Create data set
+numVoxels = 10000;
+numSubjs = 20;
+nCond = 2;
+sigEffects = 20;
+effectAmp = 3;
+
+disp(['Running simulation analysis with ' num2str(permutations) ' permutations...'])
+disp(['Running contrasts on ' num2str(numVoxels) '  voxels (' num2str(numVoxels) ' independent tests) with ' num2str(numSubjs) ' subjects'])
+disp([num2str(nCond) ' conditions, with ' num2str(sigEffects) ' significant real effets'])
+
+% Construct data set (already contrasted)
+dataSet = zeros(numVoxels,numSubjs,nCond);
+for vox=1:numVoxels
+    if vox <= sigEffects
+        dataSet(vox,:, 1) = randn(1,numSubjs) + effectAmp;
+        dataSet(vox,:, 2) = randn(1,numSubjs);
+    else
+        dataSet(vox,:, 1) = randn(1,numSubjs);
+        dataSet(vox,:, 2) = randn(1,numSubjs);
+    end
+end
+
+% Create contrast map
+contrastSet = dataSet(:,:,1) - dataSet(:,:,2);
+
+
+%% Run permutation test
+disp('Timing permutation testing using House code')
+tic
+alpha = .05;
+[t, maxT_thresh] = maxT(contrastSet,'nullmean', 0, ...
+                  'alpha',alpha,...
+                  'tail', 1, ...
+                  'permutations',permutations, ...
+                  'nproc', 20);
+toc
+
+%disp(['Number of true effects: ' num2str(sigEffects)])
+%disp(['Number of statistically significant effects (p < .05): ' num2str(sum(p_fwe>.95))])
+
+
+%% Compare with Groppe's Matlab function
+% Format data in his required format
+tmpdat = contrastSet';
+disp('Running permutations using Groppe''s Matlab function')
+tic
+[pval, t_orig, crit_t, est_alpha, seed_state]=mult_comp_perm_t1(tmpdat,permutations,1,alpha,0,0);
+toc