% [p, observeddifference, effectsize] = permutationTest(sample1, sample2, permutations [, varargin])
%
%       Permutation test (aka randomisation test), testing for a difference
%       in means between two samples. 
%
% In:
%       sample1 - vector of measurements representing one sample
%       sample2 - vector of measurements representing a second sample
%       permutations - the number of permutations
%
% Optional (name-value pairs):
%       sidedness - whether to test one- or two-sided:
%           'both' - test two-sided (default)
%           'smaller' - test one-sided, alternative hypothesis is that
%                       the mean of sample1 is smaller than the mean of
%                       sample2
%           'larger' - test one-sided, alternative hypothesis is that
%                      the mean of sample1 is larger than the mean of
%                      sample2
%       exact - whether or not to run an exact test, in which all possible
%               combinations are considered. this is only feasible for
%               relatively small sample sizes. the 'permutations' argument
%               will be ignored for an exact test. (1|0, default 0)
%       plotresult - whether or not to plot the distribution of randomised
%                    differences, along with the observed difference (1|0,
%                    default: 0)
%       showprogress - whether or not to show a progress bar. if 0, no bar
%                      is displayed; if showprogress > 0, the bar updates 
%                      every showprogress-th iteration.
%
% Out:  
%       p - the resulting p-value
%       observeddifference - the observed difference between the two
%                            samples, i.e. mean(sample1) - mean(sample2)
%       effectsize - the effect size
%
% Usage example:
%       >> permutationTest(rand(1,100), rand(1,100)-.25, 10000, ...
%          'plotresult', 1, 'showprogress', 250)
% 
%                    Copyright 2015-2018 Laurens R Krol
%                    Team PhyPA, Biological Psychology and Neuroergonomics,
%                    Berlin Institute of Technology

% 2019-02-01 lrk
%   - Added short description
%   - Increased the number of bins in the plot
% 2018-03-15 lrk
%   - Suppressed initial MATLAB:nchoosek:LargeCoefficient warning
% 2018-03-14 lrk
%   - Added exact test
% 2018-01-31 lrk
%   - Replaced calls to mean() with nanmean()
% 2017-06-15 lrk
%   - Updated waitbar message in first iteration
% 2017-04-04 lrk
%   - Added progress bar
% 2017-01-13 lrk
%   - Switched to inputParser to parse arguments
% 2016-09-13 lrk
%   - Caught potential issue when column vectors were used
%   - Improved plot
% 2016-02-17 toz
%   - Added plot functionality
% 2015-11-26 First version

% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program.  If not, see <http://www.gnu.org/licenses/>.


function [p, observeddifference, effectsize] = permutationTest(sample1, sample2, permutations, varargin)

% parsing input
p = inputParser;

addRequired(p, 'sample1', @isnumeric);
addRequired(p, 'sample2', @isnumeric);
addRequired(p, 'permutations', @isnumeric);

addParamValue(p, 'sidedness', 'both', @(x) any(validatestring(x,{'both', 'smaller', 'larger'})));
addParamValue(p, 'exact' , 0, @isnumeric);
addParamValue(p, 'plotresult', 0, @isnumeric);
addParamValue(p, 'showprogress', 0, @isnumeric);

parse(p, sample1, sample2, permutations, varargin{:})

sample1 = p.Results.sample1;
sample2 = p.Results.sample2;
permutations = p.Results.permutations;
sidedness = p.Results.sidedness;
exact = p.Results.exact;
plotresult = p.Results.plotresult;
showprogress = p.Results.showprogress;

% enforcing row vectors
if iscolumn(sample1), sample1 = sample1'; end
if iscolumn(sample2), sample2 = sample2'; end

allobservations = [sample1, sample2];
observeddifference = nanmean(sample1) - nanmean(sample2);
effectsize = observeddifference / nanmean([std(sample1), std(sample2)]);

w = warning('off', 'MATLAB:nchoosek:LargeCoefficient');
if ~exact && permutations > nchoosek(numel(allobservations), numel(sample1))
    warning(['the number of permutations (%d) is higher than the number of possible combinations (%d);\n' ...
             'consider running an exact test using the ''exact'' argument'], ...
             permutations, nchoosek(numel(allobservations), numel(sample1)));
end
warning(w);

if showprogress, w = waitbar(0, 'Preparing test...', 'Name', 'permutationTest'); end

if exact
    % getting all possible combinations
    allcombinations = nchoosek(1:numel(allobservations), numel(sample1));
    permutations = size(allcombinations, 1);
end

% running test
randomdifferences = zeros(1, permutations);
if showprogress, waitbar(0, w, sprintf('Permutation 1 of %d', permutations), 'Name', 'permutationTest'); end
for n = 1:permutations
    if showprogress && mod(n,showprogress) == 0, waitbar(n/permutations, w, sprintf('Permutation %d of %d', n, permutations)); end
    
    % selecting either next combination, or random permutation
    if exact, permutation = [allcombinations(n,:), setdiff(1:numel(allobservations), allcombinations(n,:))];
    else, permutation = randperm(length(allobservations)); end
    
    % dividing into two samples
    randomSample1 = allobservations(permutation(1:length(sample1)));
    randomSample2 = allobservations(permutation(length(sample1)+1:length(permutation)));
    
    % saving differences between the two samples
    randomdifferences(n) = nanmean(randomSample1) - nanmean(randomSample2);
end
if showprogress, delete(w); end

% getting probability of finding observed difference from random permutations
if strcmp(sidedness, 'both')
    p = (length(find(abs(randomdifferences) > abs(observeddifference)))+1) / (permutations+1);
elseif strcmp(sidedness, 'smaller')
    p = (length(find(randomdifferences < observeddifference))+1) / (permutations+1);
elseif strcmp(sidedness, 'larger')
    p = (length(find(randomdifferences > observeddifference))+1) / (permutations+1);
end

% plotting result
if plotresult
    figure;
    hist(randomdifferences, 20);
    hold on;
    xlabel('Random differences');
    ylabel('Count')
    od = plot(observeddifference, 0, '*r', 'DisplayName', sprintf('Observed difference.\nEffect size: %.2f,\np = %f', effectsize, p));
    legend(od);
end

end