Added source Matlab code for reference

matlab/spatial/private/computeTotalLogml.m

@@ -0,0 +1,42 @@
+function logml = computeTotalLogml
+% compute the log marginal likelihood of the data
+% Lu Cheng, 15.12.2012
+
+global LOGML_TABLE;
+global LOC_CQ_COUNTS;
+global LOC_SP_COUNTS;
+
+
+notEmpty = any(LOC_CQ_COUNTS,1);
+npops = length(find(notEmpty == 1));
+
+% the following codes added by Lu Cheng, 15.12.2012
+% some lines might all be zero if some sequence is deleted
+tmpIndsCq = find(any(LOC_CQ_COUNTS,2));
+tmpIndsSp = find(any(LOC_SP_COUNTS,2));
+
+locCqCounts = LOC_CQ_COUNTS(tmpIndsCq,notEmpty);
+locSpCounts = LOC_SP_COUNTS(tmpIndsSp,notEmpty);
+
+sumcliq=sum(locCqCounts, 2);
+sumsep=sum(locSpCounts, 2);
+
+ncliq = length(tmpIndsCq);
+nsep = length(tmpIndsSp);
+cliqsizes = sum(locCqCounts, 2)';
+sepsizes = sum(locSpCounts, 2)';
+cliqsizes = min([cliqsizes; npops*ones(1,ncliq)])';
+sepsizes = min([sepsizes; npops*ones(1,nsep)])';
+
+klikkitn = sum(sum(gammaln(locCqCounts + repmat(1./cliqsizes, [1 npops])))) ... 
+                    - sum(npops*(gammaln(1./cliqsizes))) ...
+                    - sum(gammaln(sumcliq + 1));
+                                    
+septn = sum(sum(gammaln(locSpCounts + repmat(1./sepsizes, [1 npops])))) ...
+                - sum(npops*(gammaln(1./sepsizes))) ...
+                - sum(gammaln(sumsep + 1));
+            
+spatialPrior = (klikkitn - septn);
+
+
+logml = sum(LOGML_TABLE) + spatialPrior;