function [s, cfg] = ft_statfun_depsamplesT(cfg, dat, design)

% FT_STATFUN_DEPSAMPLEST calculates the dependent samples t-statistic on the
% biological data (the dependent variable), using the information on the independent
% variable (ivar) in the design.
%
% Use this function by calling one of the high-level statistics functions as
%   [stat] = ft_timelockstatistics(cfg, timelock1, timelock2, ...)
%   [stat] = ft_freqstatistics(cfg, freq1, freq2, ...)
%   [stat] = ft_sourcestatistics(cfg, source1, source2, ...)
% with the following configuration option:
%   cfg.statistic = 'ft_statfun_depsamplesT'
%
% You can specify the following configuration options:
%   cfg.computestat    = 'yes' or 'no', calculate the statistic (default='yes')
%   cfg.computecritval = 'yes' or 'no', calculate the critical values of the test statistics (default='no')
%   cfg.computeprob    = 'yes' or 'no', calculate the p-values (default='no')
%
% The following options are relevant if cfg.computecritval='yes' and/or cfg.computeprob='yes':
%   cfg.alpha = critical alpha-level of the statistical test (default=0.05)
%   cfg.tail  = -1, 0, or 1, left, two-sided, or right (default=1)
%               cfg.tail in combination with cfg.computecritval='yes'
%               determines whether the critical value is computed at
%               quantile cfg.alpha (with cfg.tail=-1), at quantiles
%               cfg.alpha/2 and (1-cfg.alpha/2) (with cfg.tail=0), or at
%               quantile (1-cfg.alpha) (with cfg.tail=1)
%
% The experimental design is specified as:
%   cfg.ivar  = independent variable, row number of the design that contains the labels of the conditions to be compared (default=1)
%   cfg.uvar  = unit variable, row number of design that contains the labels of the units-of-observation, i.e. subjects or trials (default=2)
%
% The labels for the independent variable should be specified as the number 1 and 2.
% The labels for the unit of observation should be integers ranging from 1 to the
% total number of observations (subjects or trials).
%
% See also FT_TIMELOCKSTATISTICS, FT_FREQSTATISTICS or FT_SOURCESTATISTICS

% Copyright (C) 2006, Eric Maris
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
%    FieldTrip 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.
%
%    FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$

% set the defaults
cfg.computestat    = ft_getopt(cfg, 'computestat', 'yes');
cfg.computecritval = ft_getopt(cfg, 'computecritval', 'no');
cfg.computeprob    = ft_getopt(cfg, 'computeprob', 'no');
cfg.alpha          = ft_getopt(cfg, 'alpha', 0.05);
cfg.tail           = ft_getopt(cfg, 'tail', 1);
cfg.ivar           = ft_getopt(cfg, 'ivar', 1);
cfg.uvar           = ft_getopt(cfg, 'uvar', 2);

% perform some checks on the configuration
if strcmp(cfg.computeprob,'yes') && strcmp(cfg.computestat,'no')
  ft_error('P-values can only be calculated if the test statistics are calculated');
end

% perform some checks on the design
sel1 = find(design(cfg.ivar,:)==1);
sel2 = find(design(cfg.ivar,:)==2);
n1  = length(sel1);
n2  = length(sel2);
if (n1+n2)<size(design,2) || (n1~=n2)
  ft_error('Invalid specification of the design array.');
end
nunits = length(design(cfg.uvar, sel1));
df = nunits - 1;
if nunits<2
  ft_error('The data must contain at least two units of observation (trials or subjects).')
end
if (nunits*2)~=(n1+n2)
  ft_error('Invalid specification of the design array.');
end

if strcmp(cfg.computestat,'yes')
  % compute the statistic
  % store the positions of the 1-labels and the 2-labels in a nunits-by-2 array
  poslabelsperunit = zeros(nunits,2);
  poslabel1        = find(design(cfg.ivar,:)==1);
  poslabel2        = find(design(cfg.ivar,:)==2);
  [dum,i]          = sort(design(cfg.uvar,poslabel1), 'ascend');
  poslabelsperunit(:,1) = poslabel1(i);
  [dum,i]          = sort(design(cfg.uvar,poslabel2), 'ascend');
  poslabelsperunit(:,2) = poslabel2(i);

  % calculate the differences between the conditions
  diffmat = dat(:,poslabelsperunit(:,1)) - dat(:,poslabelsperunit(:,2));

  % calculate the dependent samples t-statistics
  if any(isnan(diffmat(:)))
    avgdiff = nanmean(diffmat,2);
    vardiff = nanvar(diffmat,0,2);
    nunits  = sum(~isnan(diffmat),2);
    s.stat  = (sqrt(nunits).*avgdiff)./sqrt(vardiff);
  else
    avgdiff = mean(diffmat,2);
    vardiff = var(diffmat,0,2);
    s.stat  = sqrt(nunits)*avgdiff./sqrt(vardiff);
  end
end

if strcmp(cfg.computecritval, 'yes')
  % also compute the critical values
  s.df      = df;
  if cfg.tail==-1
    s.critval = tinv(cfg.alpha,df);
  elseif  cfg.tail==0
    s.critval = [tinv(cfg.alpha/2,df),tinv(1-cfg.alpha/2,df)];
  elseif cfg.tail==1
    s.critval = tinv(1-cfg.alpha,df);
  end
end

if strcmp(cfg.computeprob, 'yes')
  % also compute the p-values
  s.df      = df;
  if cfg.tail==-1
    s.prob = tcdf(s.stat,s.df);
  elseif  cfg.tail==0
    s.prob = 2*tcdf(-abs(s.stat),s.df);
  elseif cfg.tail==1
    s.prob = 1-tcdf(s.stat,s.df);
  end
end
