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Hello community,
here is the log from the commit of package octave-forge-nan for
openSUSE:Factory checked in at 2021-09-22 22:12:56
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/octave-forge-nan (Old)
and /work/SRC/openSUSE:Factory/.octave-forge-nan.new.1899 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "octave-forge-nan"
Wed Sep 22 22:12:56 2021 rev:13 rq:920809 version:3.6.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/octave-forge-nan/octave-forge-nan.changes
2021-03-17 20:20:04.859327858 +0100
+++
/work/SRC/openSUSE:Factory/.octave-forge-nan.new.1899/octave-forge-nan.changes
2021-09-22 22:13:12.780335786 +0200
@@ -1,0 +2,6 @@
+Wed Sep 15 09:14:52 UTC 2021 - Atri Bhattacharya <badshah...@gmail.com>
+
+- Update to version 3.6.0:
+ * corrplot, knnsearch <NEW>.
+
+-------------------------------------------------------------------
Old:
----
nan-3.5.3.tar.gz
New:
----
nan-3.6.0.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ octave-forge-nan.spec ++++++
--- /var/tmp/diff_new_pack.0I1fIS/_old 2021-09-22 22:13:13.348336258 +0200
+++ /var/tmp/diff_new_pack.0I1fIS/_new 2021-09-22 22:13:13.352336261 +0200
@@ -1,5 +1,5 @@
#
-# spec file for package octave-forge-nan
+# spec file
#
# Copyright (c) 2021 SUSE LLC
#
@@ -18,7 +18,7 @@
%define octpkg nan
Name: octave-forge-%{octpkg}
-Version: 3.5.3
+Version: 3.6.0
Release: 0
Summary: A statistics and machine learning toolbox
License: GPL-3.0-or-later
++++++ nan-3.5.3.tar.gz -> nan-3.6.0.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/DESCRIPTION new/nan-3.6.0/DESCRIPTION
--- old/nan-3.5.3/DESCRIPTION 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/DESCRIPTION 2021-07-26 16:19:19.000000000 +0200
@@ -1,6 +1,6 @@
Name: NaN
-Version: 3.5.3
-Date: 2021-02-15
+Version: 3.6.0
+Date: 2021-07-26
Author: Alois Schl??gl <alois.schlo...@gmail.com>
Maintainer: Alois Schl??gl
Title: The NaN-toolbox
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/INDEX new/nan-3.6.0/INDEX
--- old/nan-3.5.3/INDEX 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/INDEX 2021-07-26 16:19:19.000000000 +0200
@@ -14,7 +14,7 @@
histo2 histo3 histo4 kolmogorov_smirnov kstest2 roc
kappa load_cifar100 load_cifar10 load_mnist
fishers_exact_test betapdf betacdf betainv
- gini lmom
+ gini lmom corrplot knnsearch
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/NEWS new/nan-3.6.0/NEWS
--- old/nan-3.5.3/NEWS 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/NEWS 2021-07-26 16:19:19.000000000 +0200
@@ -1,3 +1,8 @@
+2021-07-26: Release of NaN-toolbox 3.6.0
+
+* corrplot, knnsearch <NEW>
+
+
2021-02-15: Release of NaN-toolbox 3.5.3
* kappa: Youden index (YI), and SSE as return value
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/inst/betacdf.m new/nan-3.6.0/inst/betacdf.m
--- old/nan-3.5.3/inst/betacdf.m 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/inst/betacdf.m 2021-07-26 16:19:19.000000000 +0200
@@ -31,13 +31,23 @@
end
if (~ isscalar (a) || ~ isscalar (b))
- [retval, x, a, b] = common_size (x, a, b);
+ % [retval, x, a, b] = common_size (x, a, b);
+ retval = ~isscalar(a) && any(size(x)~=size(a));
+ retval = retval || (~isscalar(b) && any(size(x)~=size(b)));
+
if (retval > 0)
error ('betacdf: X, A, and B must be of common size or scalars');
end
end
+ if isscalar(a)
+ a = repmat(a,size(x));
+ end
+ if isscalar(b)
+ b = repmat(b,size(x));
+ end
+
- if (iscomplex (x) || iscomplex (a) || iscomplex (b))
+ if (~isreal (x) || ~isreal (a) || ~isreal (b))
error ('betacdf: X, A, and B must not be complex');
end
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/inst/betainv.m new/nan-3.6.0/inst/betainv.m
--- old/nan-3.5.3/inst/betainv.m 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/inst/betainv.m 2021-07-26 16:19:19.000000000 +0200
@@ -32,14 +32,22 @@
print_usage ();
end
- if (! isscalar (a) || ~isscalar (b))
- [retval, x, a, b] = common_size (x, a, b);
+ if (~isscalar (a) || ~isscalar (b))
+ retval = ~isscalar(a) && any(size(x)~=size(a));
+ retval = retval || (~isscalar(b) && any(size(x)~=size(b)));
+
if (retval > 0)
error ('betainv: X, A, and B must be of common size or scalars');
end
end
+ if isscalar(a)
+ a = repmat(a,size(x));
+ end
+ if isscalar(b)
+ b = repmat(b,size(x));
+ end
- if (iscomplex (x) || iscomplex (a) || iscomplex (b))
+ if (~isreal (x) || ~isreal (a) || ~isreal (b))
error ('betainv: X, A, and B must not be complex');
end
@@ -57,7 +65,7 @@
k = find ((x > 0) & (x < 1) & (a > 0) & (b > 0));
if (~ isempty (k))
- if (~ isscalar (a) || ~ isscalar (b))
+ if (~isscalar (a) || ~isscalar (b))
a = a(k);
b = b(k);
y = a ./ (a + b);
@@ -83,7 +91,7 @@
y_new = y;
loopcnt = 0;
- do
+ while (1),
y_old = y_new;
h = (betacdf (y_old, a, b) - x) ./ betapdf (y_old, a, b);
y_new = y_old - h;
@@ -96,12 +104,13 @@
y_new(ind) = 1 - (1 - y_old(ind)) / 10;
end
h = y_old - y_new;
- until (max (abs (h)) < sqrt (myeps) || ++loopcnt == 40)
+ loopcnt = loopcnt+1;
+ if ( (max(abs(h)) < sqrt(myeps)) || (loopcnt >= 40)) break; end
+ end
if (loopcnt == 40)
warning ('betainv: calculation failed to converge for some values');
end
-
inv(k) = y_new;
end
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/inst/betapdf.m new/nan-3.6.0/inst/betapdf.m
--- old/nan-3.5.3/inst/betapdf.m 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/inst/betapdf.m 2021-07-26 16:19:19.000000000 +0200
@@ -33,13 +33,23 @@
end
if (~ isscalar (a) || ~ isscalar (b))
- [retval, x, a, b] = common_size (x, a, b);
+ % [retval, x, a, b] = common_size (x, a, b);
+ retval = ~isscalar(a) && any(size(x)~=size(a));
+ retval = retval || (~isscalar(b) && any(size(x)~=size(b)));
+
if (retval > 0)
error ('betapdf: X, A, and B must be of common size or scalars');
end
end
+ if isscalar(a)
+ a = repmat(a,size(x));
+ end
+ if isscalar(b)
+ b = repmat(b,size(x));
+ end
+
- if (iscomplex (x) || iscomplex (a) || iscomplex (b))
+ if (~isreal (x) || ~isreal (a) || ~isreal (b))
error ('betapdf: X, A, and B must not be complex');
end
@@ -53,14 +63,10 @@
pdf(k) = NaN;
k = (x > 0) & (x < 1) & (a > 0) & (b > 0) & ((a ~= 1) | (b ~= 1));
- if (isscalar (a) && isscalar (b))
- pdf(k) = exp ((a - 1) * log (x(k))
- + (b - 1) * log (1 - x(k))
- + gammaln (a + b) - gammaln (a) - gammaln (b));
+ if (isscalar (a) && isscalar (b)),
+ pdf(k) = exp ((a - 1) * log (x(k)) + (b - 1) * log (1 - x(k)) + gammaln (a
+ b) - gammaln (a) - gammaln (b));
else
- pdf(k) = exp ((a(k) - 1) .* log (x(k))
- + (b(k) - 1) .* log (1 - x(k))
- + gammaln (a(k) + b(k)) - gammaln (a(k)) - gammaln (b(k)));
+ pdf(k) = exp ((a(k) - 1) .* log (x(k)) + (b(k) - 1) .* log (1 - x(k)) +
gammaln (a(k) + b(k)) - gammaln (a(k)) - gammaln (b(k)));
end
%% Most important special cases when the density is finite.
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/inst/corrplot.m
new/nan-3.6.0/inst/corrplot.m
--- old/nan-3.5.3/inst/corrplot.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.6.0/inst/corrplot.m 2021-07-26 16:19:19.000000000 +0200
@@ -0,0 +1,58 @@
+function RES = corrplot(data, varargin)
+% CORRPLOT displays the correlation plot
+%
+% corrplot(data)
+% corrplot(data,'type',TYPE)
+% [R,PValue,H] = corrplot(data,Name,Value)
+%
+% Input:
+% data
+% TYPE: 'Pearson' (default), 'Kendall', 'Spearman'
+%
+%
+% Copyright (C) 2021 by Alois Schloegl <alois.schlo...@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.
+
+Mode=[];
+alpha=0.05;
+
+k=1;
+while k<=nargin,
+ if strcmpi(varargin{k},'type')
+ Mode=varargin{k+1};
+ k=k+1;
+ elseif strcmpi(varargin{k},'alpha')
+ alpha=varargin{k+1};
+
+ end
+
+ k=k+1;
+end
+
+[nr,nc]=size(data);
+
+for k1=1:nc
+for k2=1:nc
+ subplot(nc,nc,k1*nc+k2-nc)
+ plot(data(:,k1),data(:,k2),'d')
+end
+end
+
+R = corrcoef(data);
+
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/inst/knnsearch.m
new/nan-3.6.0/inst/knnsearch.m
--- old/nan-3.5.3/inst/knnsearch.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.6.0/inst/knnsearch.m 2021-07-26 16:19:19.000000000 +0200
@@ -0,0 +1,166 @@
+function [idx, dist]=knnsearch(X,Y,varargin)
+% KNNSEARCH search for K nearest neighbors
+% and related statistics
+%
+% Usage:
+% IDX = knnsearch(X,Y);
+% finds for each element (row) in Y, the nearest
+% of all elements in X, such that
+% IDX(k) points to X(IDX(k),:) that is nearest to Y(k,:)
+% IDX has as many elements as Y has rows
+% [IDX,DIST] = knnsearch(X,Y);
+% ... = knnsearch(...,'k',k);
+% search for k nearest neighbors (default: k=2)
+% ... = knnsearch(...,'Scale',Scale);
+% Scaling vector of 'seuclidian' metric
+% default value is std(X)
+% ... = knnsearch(...,'Cov',Cov);
+% Cov is the covariance matrix used for Mahalanobis distance
+% default value is cov(X)
+% ... = knnsearch(...,'Distance',Distance);
+% the following distance metrics are currently supported:
+% 'euclidean' [1],
+% 'seuclidean', (scaled euclidian)
+% 'minkowski' [3],
+% 'cityblock' or 'manhattan' [4],
+% 'hamming' [5],
+% 'mahalanobis' [6],
+% 'cosine' [7]
+% (one minus the cosine of the angle between the two samples),
+% 'correlation'
+% (one minus the linear correlation between each pair f data
vectors),
+% 'spearman'
+% (one minus the rank correlation between each pair of data
vectors),
+%
+% SEE ALSO: corrcoef, spearman, rankcorr, cov, std
+%
+% Reference(s):
+% [1] https://en.wikipedia.org/wiki/K-nearest_neighbors_algorithm
+% [2] https://en.wikipedia.org/wiki/Euclidean_distance
+% [3] https://en.wikipedia.org/wiki/Minkowski_distance
+% [4] https://en.wikipedia.org/wiki/Taxicab_geometry
+% [5] https://en.wikipedia.org/wiki/Hamming_distance
+% [6] https://en.wikipedia.org/wiki/Mahalanobis_distance
+% [7] https://en.wikipedia.org/wiki/Cosine_similarity
+
+% Copyright (C) 2021 by Alois Schloegl <alois.schlo...@gmail.com>
+% This function is part of the NaN-toolbox
+% http://pub.ist.ac.at/~schloegl/matlab/NaN/
+%
+% BioSig 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.
+%
+% BioSig 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 BioSig. If not, see <http://www.gnu.org/licenses/>.
+
+
+if nargin<2
+ error('missing input arguments')
+end
+
+if size(X,2)~=size(Y,2)
+ error('number of rows in X and Y must match')
+end
+
+% default values
+K=1; # number of NN
+P=2; # exponent for minkowski distance
+Distance='euclidean';
+NSMethod='exhaustive';
+Scale = [];
+Cov = [];
+
+k=1;
+while (k<length(varargin))
+ if strcmpi(varargin{k},'k')
+ K = varargin{k+1};
+ k=k+2;
+ continue;
+ elseif strcmp(varargin{k},'P')
+ P = varargin{k+1};
+ k=k+2;
+ continue;
+ elseif strcmp(varargin{k},'Scale')
+ Scale = varargin{k+1};
+ if (length(Scale)~=size(X,2))
+ error('size of Cov does not match input data');
+ end
+ k=k+2;
+ continue;
+ elseif strcmp(varargin{k},'Cov')
+ Cov = varargin{k+1};
+ if ~all(size(Cov)==size(X,2))
+ error('size of Cov does not match input data');
+ end
+ k=k+2;
+ continue;
+ elseif strcmpi(varargin{k},'Distance')
+ Distance = varargin{k+1};
+ k=k+2;
+ continue;
+ elseif strcmpi(varargin{k},'NSMethod')
+ NSMethod = varargin{k+1};
+ k=k+2;
+ continue;
+ else
+ disp(varargin{k});
+ fprintf(1,'Warning: input argument is ignored');
+ end
+ k=k+1;
+end
+
+[ix,iy]=meshgrid(1:size(X,1),1:size(Y,1));
+if strcmp(Distance,'euclidean')
+ D = sqrt(sum((X(ix(:),:)-Y(iy(:),:)).^2,2));
+
+elseif strcmp(Distance,'seuclidean')
+ if isempty(Scale), Scale=std(X,[],1); end;
+ IS = Scale(:).^(-2);
+ dxy = X(ix(:),:) - Y(iy(:),:);
+ D = sqrt((dxy.^2)*IS);
+
+elseif strcmp(Distance,'mahalanobis')
+ if isempty(Cov), Cov=cov(X(~any(isnan(X),2),:)); end;
+ dxy = X(ix(:),:)-Y(iy(:),:);
+ D = sqrt( sum( (dxy*inv(Cov)).*dxy, 2) );
+
+elseif strcmp(Distance,'minkowski')
+ D = sum(abs(X(ix(:),:)-Y(iy(:),:)).^P,2).^(1/P);
+
+elseif strcmp(Distance,'cityblock') || strcmp(Distance,'manhattan')
+ D = sum(abs(X(ix(:),:)-Y(iy(:),:)),2);
+
+elseif strcmp(Distance,'cosine')
+ sx = sum(X.^2, 2).^(-1/2);
+ sy = sum(Y.^2, 2).^(-1/2);
+ D = 1 - sum(X(ix(:),:).*Y(iy(:),:), 2).*sx(ix(:)).*sy(iy(:));
+
+elseif strcmp(Distance,'correlation')
+ D = 1 - corrcoef(Y', X');
+
+elseif strcmp(Distance,'spearman')
+ D = 1 - corrcoef(Y', X', 'Rank');
+
+elseif strcmp(Distance,'hamming')
+ D = mean(abs(X(ix(:),:)~=Y(iy(:),:)),2);
+
+elseif 0, % add more
+else
+ error(sprintf('distance metric "%s" not supported yet',Distance));
+end
+
+D = reshape(D,size(Y,1),size(X,1));
+if K==1,
+ [dist,idx]=min(D,[],2);
+else
+ [dist,idx]=sort(D,2);
+ dist=dist(:,1:K);
+ idx=idx(:,1:K);
+end
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.3/inst/naninsttest.m
new/nan-3.6.0/inst/naninsttest.m
--- old/nan-3.5.3/inst/naninsttest.m 2021-02-15 07:41:05.000000000 +0100
+++ new/nan-3.6.0/inst/naninsttest.m 2021-07-26 16:19:19.000000000 +0200
@@ -22,9 +22,9 @@
% along with this program; If not, see <http://www.gnu.org/licenses/>.
-r = zeros(38,2);
+r = zeros(42,2);
-x = [5,NaN,0,1,nan];
+x = [5,NaN,0,1,nan,-1:.4:1];
% run test, k=1: with NaNs, k=2: all NaN's are removed
% the result of both should be the same.
@@ -32,7 +32,7 @@
%FLAG_WARNING = warning;
warning('off');
-funlist =
{'sumskipnan','mean','std','var','skewness','kurtosis','sem','median','mad','zscore','coefficient_of_variation','geomean','harmmean','meansq','moment','rms','','corrcoef','rankcorr','spearman','ranks','center','trimean','min','max','tpdf','tcdf','tinv','normpdf','normcdf','norminv','nansum','nanstd','histo_mex','sumskipnan_mex','covm_mex','svmtrain_mex','train','','','','','','','',''};
+funlist =
{'sumskipnan','mean','std','var','skewness','kurtosis','sem','median','mad','zscore','coefficient_of_variation','geomean','harmmean','meansq','moment','rms','','corrcoef','rankcorr','spearman','ranks','center','trimean','min','max','tpdf','tcdf','tinv','normpdf','normcdf','norminv','nansum','nanstd','histo_mex','sumskipnan_mex','covm_mex','svmtrain_mex','train','ttest','betapdf','betacdf','betainv','','','',''};
for k=1:2,
if k==2, x(isnan(x))=[]; end;
r(1,k) =sumskipnan(x(1));
@@ -147,6 +147,16 @@
if exist('ttest','file'),
r(39,k)=ttest([x,x,x],10);
end;
+
+ if exist('betapdf','file'),
+ r(40,k)=sum(~isnan(betapdf([x,x,x],10,5)));
+ end;
+ if exist('betacdf','file'),
+ r(41,k)=sum(~isnan(betapdf([x,x,x],10,5)));
+ end;
+ if exist('betainv','file'),
+ r(42,k)=sum(~isnan(betainv([x,x,x],10,5)));
+ end;
end;
% check if result is correct
