merged the new master, resolved conflicts

Author: paulstapor

.gitignore

@@ -14,5 +14,5 @@ doc/config/latexextras.sty
 doc/config/mtocpp_filter.sh
 DRAMToolbox
 *.asv
-examples\RAmPART_examples\results
+examples/RAmPART_examples/results
 

@PestoOptions/PestoOptions.m

@@ -419,9 +419,9 @@
             end
 
             % Add required subclasses
-%             obj.MCMC = PestoSamplingOptions();
-%             obj.HO = HOOptions;
-%             obj.HO.foldername = obj.foldername;
+            obj.MCMC = PestoSamplingOptions();
+            obj.HO = HOOptions;
+            obj.HO.foldername = obj.foldername;
 
         end
 

@PestoSamplingOptions/PestoSamplingOptions.m

@@ -69,8 +69,10 @@
       saveFileName = '';
       saveEach = 0;
 
-      % Parallel Tempering Options, an instance of PTOptions
-      PT;
+      % Parallel Tempering Options, an instance of PTOptions - this
+      % instance is also used for initalization in case no algorithm was
+      % specified
+      PT = PTOptions(); 
 
       % Parallel Hierarchical Sampling options, an instance of PHSOptions
       PHS;
@@ -322,20 +324,22 @@
             end
 
          else
-            warning('No user-provided initial point found. Setting Initial points randomly.')
+            warning('No user-provided initial point found. Setting Initial points randomly.')    
+            par.min = par.min(:);
+            par.max = par.max(:);
             switch this.samplingAlgorithm
                case {'DRAM','MALA'}
-                  this.theta0 = bsxfun(@plus, par.min', ...
-                     bsxfun(@times, par.max' - par.min', rand(par.number,1)))';
+                  this.theta0 = bsxfun(@plus, par.min, ...
+                     bsxfun(@times, par.max - par.min, rand(par.number,1)));
                case 'PT'
-                  this.theta0 = bsxfun(@plus, par.min', ...
-                     bsxfun(@times, par.max' - par.min', rand(par.number,this.PT.nTemps)))';
+                  this.theta0 = bsxfun(@plus, par.min, ...
+                     bsxfun(@times, par.max - par.min, rand(par.number,this.PT.nTemps)));
                case 'PHS'
-                  this.theta0 = bsxfun(@plus, par.min', ...
-                     bsxfun(@times, par.max' - par.min', rand(par.number,this.PHS.nChains)))';
+                  this.theta0 = bsxfun(@plus, par.min, ...
+                     bsxfun(@times, par.max - par.min, rand(par.number,this.PHS.nChains)));
                case 'RAMPART'
-                  this.theta0 = bsxfun(@plus, par.min', ...
-                     bsxfun(@times, par.max' - par.min', rand(par.number,this.RAMPART.nTemps)))';                  
+                  this.theta0 = bsxfun(@plus, par.min, ...
+                     bsxfun(@times, par.max - par.min, rand(par.number,this.RAMPART.nTemps)));                  
             end
          end
          if ~isempty(this.sigma0)

…achmann_JakStat/logLikelihood_Bachmann.m …JakStat/logLikelihood_Bachmann_rampart.mexamples/RAmPART_examples/Bachmann_JakStat/logLikelihood_Bachmann.m renamed to examples/RAmPART_examples/Bachmann_JakStat/logLikelihood_Bachmann_rampart.m examples/RAmPART_examples/Bachmann_JakStat/logLikelihood_Bachmann.m renamed to examples/RAmPART_examples/Bachmann_JakStat/logLikelihood_Bachmann_rampart.m

@@ -36,7 +36,7 @@
    % distributed
    m = length(par);
    for i = p+1:m
-      llh = llh + log(normpdf(par(i),25,1));
+      llh = llh - log(1*sqrt(2*pi)) - 0.5 * ((par(i)-25)/1)^2; 
    end
 
 end