small tweaks to run_me()

demo/run_me.m

@@ -81,12 +81,11 @@
 % See also: Data, Model
 
 % --------- USE THE CODE BELOW AS A TEMPLATE FOR YOUR OWN ANALYSES --------
-
-% USERS TO REPLACE THIS CODE... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+% USERS TO REPLACE THIS CODE BLOCK ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 path_of_this_mfile = strrep(which(mfilename),[mfilename '.m'],'');
 toolbox_path = fullfile(path_of_this_mfile,'..','ddToolbox');
 datapath = fullfile(path_of_this_mfile,'datasets','kirby');
-% ...WITH THIS (update the paths as appropriate) ~~~~~~~~~~~~~~~~~~~~~~~~~~
+% WITH THIS (update the paths as appropriate) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 % addpath('~/git-local/delay-discounting-analysis/ddToolbox')
 % datapath = '~/git-local/delay-discounting-analysis/demo/data';
 % ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -96,14 +95,26 @@
 ddAnalysisSetUp();
 
 % Do an analysis
-model = ModelMixedME(...
+model = ModelHierarchicalME(...
 	Data(datapath, 'files', allFilesInFolder(datapath, 'txt')),...
 	'savePath', fullfile(pwd,'output','my_analysis'),...
-	'pointEstimateType','median',...
+	'pointEstimateType', 'median',...
 	'sampler', 'jags',...
-	'shouldPlot', 'no',...
-	'mcmcParams', struct('nsamples', 500,...
-						 'chains', 2,...
-	 					 'nburnin', 100));
+	'shouldPlot', 'yes',...
+	'shouldExportPlots', true,...
+	'mcmcParams', struct('nsamples', 5000,...
+						 'chains', 4,...
+	 					 'nburnin', 1000));
+
+% NOTE:
+% - you will want to increase the 'nburnin' and 'nsamples' when you are
+% running proper analyses. I have provided small numbers here just to
+% confirm the code is working without having to wait a long time.
+% - you can change the point estimate type to mean, median, or mode
+% - the sampler can be 'jags' or 'stan', although stan models are not yet
+% full complete
+
 
-% model.plot('shouldExportPlots', false)
+% If we didn't ask for plots when we ran the model, then we do that
+% after with this command...
+%	model.plot('shouldExportPlots', false)

runalltests.m

@@ -1,4 +1,4 @@
-%RUNALLTESTS
+%runalltests
 % A script to run the tests
 %
 % Manually run specific tests like this...