X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=octave_packages%2Fnan-2.5.5%2Fbland_altman.m;fp=octave_packages%2Fnan-2.5.5%2Fbland_altman.m;h=516026b439605c85597b3cfd1f7de1cf4f2a1db7;hb=c880e8788dfc484bf23ce13fa2787f2c6bca4863;hp=0000000000000000000000000000000000000000;hpb=1705066eceaaea976f010f669ce8e972f3734b05;p=CreaPhase.git

diff --git a/octave_packages/nan-2.5.5/bland_altman.m b/octave_packages/nan-2.5.5/bland_altman.m
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+function RES = bland_altman(data,group,arg3)
+% BLAND_ALTMANN shows the Bland-Altman plot of two columns of measurements
+%   and computes several summary results. 
+%
+%   bland_altman(m1, m2 [,group])
+%   bland_altman(data [, group])
+%   R = bland_altman(...)
+% 
+%   m1,m2 are two colums with the same number of elements
+%	containing the measurements. m1,m2 can be also combined 
+%       in a single two column data matrix. 
+%   group [optional] indicates which measurements belong to the same group
+%	This is useful to account for repeated measurements.  
+%
+%
+% References:
+% [1] JM Bland and DG Altman, Measuring agreement in method comparison studies. 
+%       Statistical Methods in Medical Research, 1999; 8; 135. 
+%       doi:10.1177/09622802990080204
+% [2] P.S. Myles, Using the Bland– Altman method to measure agreement with repeated measures
+%	British Journal of Anaesthesia 99(3):309–11 (2007)
+%	doi:10.1093/bja/aem214
+
+%	$Id$
+%	Copyright (C) 2010,2011 by Alois Schloegl <alois.schloegl@gmail.com>	
+%       This function is part of the NaN-toolbox
+%       http://pub.ist.ac.at/~schloegl/matlab/NaN/
+
+% 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, write to the Free Software
+% Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA 02110-1301, USA.
+
+if nargin<2, group = []; end;
+if nargin<3, arg3 = []; end;
+
+if (size(data,2)==1)
+	data  = [data, group];
+	group = arg3;
+end; 		
+
+
+D = data * [1;-1];
+M = data * [1;1]/2;
+
+RES.corrcoef = corrcoef(data(:,1),data(:,2),'spearman');
+[REs.cc,RES.p] = corrcoef(M,D,'spearman');
+if (RES.p<0.05)
+	warning('A regression model according to section 3.2 [1] should be used');
+	%% TODO: implement support for this type of data. 	
+	RES.a = [ones(size(data,1),1),D]\M;
+	RES.b = [ones(size(data,1),1),M]\D;
+end; 	
+
+if isempty(group)
+	G = [1:size(data,1)]';
+	m = ones(size(data,1),1);
+	d = D;
+	RES.Bias = mean(d,1);
+	RES.Var  = var(d);
+	
+elseif ~isempty(group)
+	%% TODO: this is not finished  	
+	warning('analysis of data with repetitions is experimental - it might yield incorrect results - you are warned.!')
+	[G,I,J] = unique (group);
+	R       = zeros(size(data));
+	m       = repmat(NaN,length(G),1);
+	n       = repmat(NaN,length(G),1);
+	d       = repmat(NaN,length(G),1);
+	d2      = repmat(NaN,length(G),1);
+	data2   = repmat(NaN,length(G),size(data,2));
+	SW2     = repmat(NaN,length(G),size(data,2));
+	for i   = 1:length(G),
+		ix         = find(group==G(i));
+		n(i)       = length(ix);
+%		IX((i-1)*N+1:i*N) = ix(ceil(rand(N,1)*n(i)));		
+		
+		[R(ix,:), data2(i,:)] = center(data(ix,:),1);
+		d(i)       = mean(D(ix,:),1);
+		m(i)       = mean(M(ix,:),1);
+		d2(i)      = mean(D(ix,:).^2,1);
+		RES.SW2(i,:)   = var(data(ix,:),[],1);
+		RES.avg(i,:)   = mean(data(ix,:),1);
+	end;
+
+	W = 1./n(J);
+	RES.SSW = sumskipnan(R.^2,1,W);
+	RES.SSB = var(data,[],1,W)*sum(W)*(sum(W)-1);
+	RES.sigma2_w= RES.SSW/(sum(W)*(length(G)-1));
+	RES.sigma2_u= RES.SSB/(sum(W)*(length(G)-1)) - RES.sigma2_w/(length(G));
+	RES.group = bland_altman(data2); 	% FIXME: this plot shows incorrect interval, it does not account for the group/repeated samples. 
+	RES.repeatability_coefficient1 = 2.77*sqrt(var(R,1,1)); 	% variance with factor group removed
+	RES.repeatability_coefficient = 2.77*sqrt(mean(SW2,1)); 	% variance with factor group removed
+	RES.std_d_ = std(d);
+	RES.std_D_ = std(D);
+	RES.std_m_ = std(m);	
+	
+	RES.n = n;
+	return; 
+
+	D = d; 
+	M = m;
+%	RES.sigma2_dw = 
+
+	RES.Bias = mean(d,1,[],n);
+end; 
+
+
+plot(M,D,'o', [min(M),max(M)]', [0,0]','k--', [min(M),max(M)]', [1,1,1; 0,1.96,-1.96]'*[RES.Bias;std(D)]*[1,1], 'k-');
+xlabel('mean');
+ylabel('difference');
+