Hello community,
here is the log from the commit of package octave-forge-nan for
openSUSE:Factory checked in at 2020-12-04 21:27:55
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/octave-forge-nan (Old)
and /work/SRC/openSUSE:Factory/.octave-forge-nan.new.5913 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "octave-forge-nan"
Fri Dec 4 21:27:55 2020 rev:11 rq:849235 version:3.5.2
Changes:
--------
--- /work/SRC/openSUSE:Factory/octave-forge-nan/octave-forge-nan.changes
2020-08-17 12:05:49.734709261 +0200
+++
/work/SRC/openSUSE:Factory/.octave-forge-nan.new.5913/octave-forge-nan.changes
2020-12-04 21:27:56.902078371 +0100
@@ -1,0 +2,14 @@
+Sun Nov 15 20:54:21 UTC 2020 - Atri Bhattacharya <[email protected]>
+
+- Update to version 3.5.2:
+ * New functions added:
+ - gini: Gini index.
+ - lmom: L-moments.
+ - betapdf, betacdf, betainv: beta distribution functions.
+ * Bug fixes:
+ - bland-altman: fix ylabel.
+ - fix debian bug #964210: test tries to download data.
+ - fix #59335: "'load_fisheriris' fails on Windows".
+ - fix #59336: "(nan) BIST for `ttest` fails".
+
+-------------------------------------------------------------------
Old:
----
nan-3.5.0.tar.gz
New:
----
nan-3.5.2.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ octave-forge-nan.spec ++++++
--- /var/tmp/diff_new_pack.le0hlj/_old 2020-12-04 21:27:57.542079290 +0100
+++ /var/tmp/diff_new_pack.le0hlj/_new 2020-12-04 21:27:57.546079295 +0100
@@ -18,7 +18,7 @@
%define octpkg nan
Name: octave-forge-%{octpkg}
-Version: 3.5.0
+Version: 3.5.2
Release: 0
Summary: A statistics and machine learning toolbox
License: GPL-3.0-or-later
++++++ nan-3.5.0.tar.gz -> nan-3.5.2.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/DESCRIPTION new/nan-3.5.2/DESCRIPTION
--- old/nan-3.5.0/DESCRIPTION 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/DESCRIPTION 2020-10-31 17:44:32.000000000 +0100
@@ -1,11 +1,11 @@
Name: NaN
-Version: 3.5.0
-Date: 2020-07-12
-Author: Alois Schloegl <[email protected]>
-Maintainer: Alois Schloegl
+Version: 3.5.2
+Date: 2020-10-31
+Author: Alois Schlögl <[email protected]>
+Maintainer: Alois Schlögl
Title: The NaN-toolbox
Description: A statistics and machine learning toolbox for data with and w/o
missing values
-Depends: octave (>= 3.8.0)
+Depends: octave (>= 4.4.1)
License: GPLv3+
Url: http://pub.ist.ac.at/~schloegl/matlab/NaN
Autoload: no
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/INDEX new/nan-3.5.2/INDEX
--- old/nan-3.5.0/INDEX 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/INDEX 2020-10-31 17:44:32.000000000 +0100
@@ -13,6 +13,8 @@
bland_altman cumsumskipnan range signrank histo
histo2 histo3 histo4 kolmogorov_smirnov kstest2 roc
kappa load_cifar100 load_cifar10 load_mnist
- fishers_exact_test
+ fishers_exact_test betapdf betacdf betainv
+ gini lmom
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/NEWS new/nan-3.5.2/NEWS
--- old/nan-3.5.0/NEWS 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/NEWS 2020-10-31 17:44:32.000000000 +0100
@@ -1,3 +1,24 @@
+
+2020-10-31: Release of NaN-toolbox 3.5.2
+
+* new functions added
+ gini: Gini index
+ lmom: L-moments
+ betapdf, betacdf, betainv:
+ beta distribution functions
+
+* bug fixes:
+ bland-altman: fix ylabel
+ fix debian bug #964210: test tries to download data
+ fix #59335: "'load_fisheriris' fails on Windows"
+ fix #59336: "(nan) BIST for `ttest` fails"
+ this failed because betainv(...) is not available
+ the suggestion of add a dependency on statistics package
+ does not work, because of a conflict with statistics
+ (it would not handle NaNs in the indended way).
+ Therefore, functions for beta* distributions are included.
+
+
2020-07-12: Release of NaN-toolbox 3.5.0
* ttest:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/betacdf.m new/nan-3.5.2/inst/betacdf.m
--- old/nan-3.5.0/inst/betacdf.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.5.2/inst/betacdf.m 2020-10-31 17:44:32.000000000 +0100
@@ -0,0 +1,89 @@
+%% Copyright (C) 2012 Rik Wehbring
+%% Copyright (C) 1995-2016 Kurt Hornik
+%%
+%% 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; see the file COPYING. If not, see
+%% <http://www.gnu.org/licenses/>.
+
+%% cdf = betacdf (x, a, b)
+%% For each element of @var{x}, compute the cumulative distribution function
+%% (CDF) at x of the Beta distribution with parameters a and b.
+
+%% Author: KH <[email protected]>
+%% Description: CDF of the Beta distribution
+
+%% Adapted for the use with Matlab and the NaN-toolbox.
+
+function cdf = betacdf (x, a, b)
+
+ if (nargin ~= 3)
+ print_usage ();
+ end
+
+ if (~ isscalar (a) || ~ isscalar (b))
+ [retval, x, a, b] = common_size (x, a, b);
+ if (retval > 0)
+ error ('betacdf: X, A, and B must be of common size or scalars');
+ end
+ end
+
+ if (iscomplex (x) || iscomplex (a) || iscomplex (b))
+ error ('betacdf: X, A, and B must not be complex');
+ end
+
+ if (isa (x, 'single') || isa (a, 'single') || isa (b, 'single'))
+ cdf = zeros (size (x), 'single');
+ else
+ cdf = zeros (size (x));
+ end
+
+ k = isnan (x) | ~(a > 0) | ~(b > 0);
+ cdf(k) = NaN;
+
+ k = (x >= 1) & (a > 0) & (b > 0);
+ cdf(k) = 1;
+
+ k = (x > 0) & (x < 1) & (a > 0) & (b > 0);
+ if (isscalar (a) && isscalar (b))
+ cdf(k) = betainc (x(k), a, b);
+ else
+ cdf(k) = betainc (x(k), a(k), b(k));
+ end
+
+end
+
+
+%!shared x,y
+%! x = [-1 0 0.5 1 2];
+%! y = [0 0 0.75 1 1];
+%!assert (betacdf (x, ones (1,5), 2*ones (1,5)), y)
+%!assert (betacdf (x, 1, 2*ones (1,5)), y)
+%!assert (betacdf (x, ones (1,5), 2), y)
+%!assert (betacdf (x, [0 1 NaN 1 1], 2), [NaN 0 NaN 1 1])
+%!assert (betacdf (x, 1, 2*[0 1 NaN 1 1]), [NaN 0 NaN 1 1])
+%!assert (betacdf ([x(1:2) NaN x(4:5)], 1, 2), [y(1:2) NaN y(4:5)])
+
+%% Test class of input preserved
+%!assert (betacdf ([x, NaN], 1, 2), [y, NaN])
+%!assert (betacdf (single ([x, NaN]), 1, 2), single ([y, NaN]))
+%!assert (betacdf ([x, NaN], single (1), 2), single ([y, NaN]))
+%!assert (betacdf ([x, NaN], 1, single (2)), single ([y, NaN]))
+
+%% Test input validation
+%!error betacdf ()
+%!error betacdf (1)
+%!error betacdf (1,2)
+%!error betacdf (1,2,3,4)
+%!error betacdf (ones (3), ones (2), ones (2))
+%!error betacdf (ones (2), ones (3), ones (2))
+%!error betacdf (ones (2), ones (2), ones (3))
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/betainv.m new/nan-3.5.2/inst/betainv.m
--- old/nan-3.5.0/inst/betainv.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.5.2/inst/betainv.m 2020-10-31 17:44:32.000000000 +0100
@@ -0,0 +1,136 @@
+%% Copyright (C) 2012 Rik Wehbring
+%% Copyright (C) 1995-2016 Kurt Hornik
+%% Copyright (C) 2020 Alois Schlögl
+%%
+%% 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; see the file COPYING. If not, see
+%% <http://www.gnu.org/licenses/>.
+
+%% inv = betainv (x, a, b)
+%% For each element of x, compute the quantile (the inverse of the CDF)
+%% at x of the Beta distribution with parameters a and b.
+
+%% Author: KH <[email protected]>
+%% Description: Quantile function of the Beta distribution
+
+%% Adapted for the use with Matlab and the NaN-toolbox.
+
+
+function inv = betainv (x, a, b)
+
+ if (nargin ~= 3)
+ print_usage ();
+ end
+
+ if (! isscalar (a) || ~isscalar (b))
+ [retval, x, a, b] = common_size (x, a, b);
+ if (retval > 0)
+ error ('betainv: X, A, and B must be of common size or scalars');
+ end
+ end
+
+ if (iscomplex (x) || iscomplex (a) || iscomplex (b))
+ error ('betainv: X, A, and B must not be complex');
+ end
+
+ if (isa (x, 'single') || isa (a, 'single') || isa (b, 'single'))
+ inv = zeros (size (x), 'single');
+ else
+ inv = zeros (size (x));
+ end
+
+ k = (x < 0) | (x > 1) | ~(a > 0) | ~(b > 0) | isnan (x);
+ inv(k) = NaN;
+
+ k = (x == 1) & (a > 0) & (b > 0);
+ inv(k) = 1;
+
+ k = find ((x > 0) & (x < 1) & (a > 0) & (b > 0));
+ if (~ isempty (k))
+ if (~ isscalar (a) || ~ isscalar (b))
+ a = a(k);
+ b = b(k);
+ y = a ./ (a + b);
+ else
+ y = a / (a + b) * ones (size (k));
+ end
+ x = x(k);
+
+ if (isa (y, 'single'))
+ myeps = eps ('single');
+ else
+ myeps = eps;
+ end
+
+ l = find (y < myeps);
+ if (any (l))
+ y(l) = sqrt (myeps) * ones (length (l), 1);
+ end
+ l = find (y > 1 - myeps);
+ if (any (l))
+ y(l) = 1 - sqrt (myeps) * ones (length (l), 1);
+ end
+
+ y_new = y;
+ loopcnt = 0;
+ do
+ y_old = y_new;
+ h = (betacdf (y_old, a, b) - x) ./ betapdf (y_old, a, b);
+ y_new = y_old - h;
+ ind = find (y_new <= myeps);
+ if (any (ind))
+ y_new(ind) = y_old(ind) / 10;
+ end
+ ind = find (y_new >= 1 - myeps);
+ if (any (ind))
+ y_new(ind) = 1 - (1 - y_old(ind)) / 10;
+ end
+ h = y_old - y_new;
+ until (max (abs (h)) < sqrt (myeps) || ++loopcnt == 40)
+
+ if (loopcnt == 40)
+ warning ('betainv: calculation failed to converge for some values');
+ end
+
+ inv(k) = y_new;
+ end
+
+end
+
+
+%!shared x
+%! x = [-1 0 0.75 1 2];
+%!assert (betainv (x, ones (1,5), 2*ones (1,5)), [NaN 0 0.5 1 NaN], eps)
+%!assert (betainv (x, 1, 2*ones (1,5)), [NaN 0 0.5 1 NaN], eps)
+%!assert (betainv (x, ones (1,5), 2), [NaN 0 0.5 1 NaN], eps)
+%!assert (betainv (x, [1 0 NaN 1 1], 2), [NaN NaN NaN 1 NaN])
+%!assert (betainv (x, 1, 2*[1 0 NaN 1 1]), [NaN NaN NaN 1 NaN])
+%!assert (betainv ([x(1:2) NaN x(4:5)], 1, 2), [NaN 0 NaN 1 NaN])
+
+%% Test class of input preserved
+%!assert (betainv ([x, NaN], 1, 2), [NaN 0 0.5 1 NaN NaN], eps)
+%!assert (betainv (single ([x, NaN]), 1, 2), single ([NaN 0 0.5 1 NaN NaN]))
+%!assert (betainv ([x, NaN], single (1), 2), single ([NaN 0 0.5 1 NaN NaN]),
eps('single'))
+%!assert (betainv ([x, NaN], 1, single (2)), single ([NaN 0 0.5 1 NaN NaN]),
eps('single'))
+
+%% Test input validation
+%!error betainv ()
+%!error betainv (1)
+%!error betainv (1,2)
+%!error betainv (1,2,3,4)
+%!error betainv (ones (3), ones (2), ones (2))
+%!error betainv (ones (2), ones (3), ones (2))
+%!error betainv (ones (2), ones (2), ones (3))
+%!error betainv (i, 2, 2)
+%!error betainv (2, i, 2)
+%!error betainv (2, 2, i)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/betapdf.m new/nan-3.5.2/inst/betapdf.m
--- old/nan-3.5.0/inst/betapdf.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.5.2/inst/betapdf.m 2020-10-31 17:44:32.000000000 +0100
@@ -0,0 +1,130 @@
+%% Copyright (C) 2012 Rik Wehbring
+%% Copyright (C) 1995-2016 Kurt Hornik
+%% Copyright (C) 2010 Christos Dimitrakakis
+%% Copyright (C) 2020 Alois Schlögl
+%%
+%% 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; see the file COPYING. If not, see
+%% <http://www.gnu.org/licenses/>.
+
+%% pdf = betapdf (x, a, b)
+%% For each element of x, compute the probability density function (PDF)
+%% at x of the Beta distribution with parameters a and b.
+
+%% Author: KH <[email protected]>, CD <[email protected]>
+%% Description: PDF of the Beta distribution
+
+%% Adapted for the use with Matlab and the NaN-toolbox.
+
+function pdf = betapdf (x, a, b)
+
+ if (nargin ~= 3)
+ print_usage ();
+ end
+
+ if (~ isscalar (a) || ~ isscalar (b))
+ [retval, x, a, b] = common_size (x, a, b);
+ if (retval > 0)
+ error ('betapdf: X, A, and B must be of common size or scalars');
+ end
+ end
+
+ if (iscomplex (x) || iscomplex (a) || iscomplex (b))
+ error ('betapdf: X, A, and B must not be complex');
+ end
+
+ if (isa (x, 'single') || isa (a, 'single') || isa (b, 'single'));
+ pdf = zeros (size (x), 'single');
+ else
+ pdf = zeros (size (x));
+ end
+
+ k = ~(a > 0) | ~(b > 0) | isnan (x);
+ 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));
+ 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)));
+ end
+
+ %% Most important special cases when the density is finite.
+ k = (x == 0) & (a == 1) & (b > 0) & (b ~= 1);
+ if (isscalar (a) && isscalar (b))
+ pdf(k) = exp (gammaln (a + b) - gammaln (a) - gammaln (b));
+ else
+ pdf(k) = exp (gammaln (a(k) + b(k)) - gammaln (a(k)) - gammaln (b(k)));
+ end
+
+ k = (x == 1) & (b == 1) & (a > 0) & (a ~= 1);
+ if (isscalar (a) && isscalar (b))
+ pdf(k) = exp (gammaln (a + b) - gammaln (a) - gammaln (b));
+ else
+ pdf(k) = exp (gammaln (a(k) + b(k)) - gammaln (a(k)) - gammaln (b(k)));
+ end
+
+ k = (x >= 0) & (x <= 1) & (a == 1) & (b == 1);
+ pdf(k) = 1;
+
+ %% Other special case when the density at the boundary is infinite.
+ k = (x == 0) & (a < 1);
+ pdf(k) = Inf;
+
+ k = (x == 1) & (b < 1);
+ pdf(k) = Inf;
+
+end
+
+
+%!shared x,y
+%! x = [-1 0 0.5 1 2];
+%! y = [0 2 1 0 0];
+%!assert (betapdf (x, ones (1,5), 2*ones (1,5)), y)
+%!assert (betapdf (x, 1, 2*ones (1,5)), y)
+%!assert (betapdf (x, ones (1,5), 2), y)
+%!assert (betapdf (x, [0 NaN 1 1 1], 2), [NaN NaN y(3:5)])
+%!assert (betapdf (x, 1, 2*[0 NaN 1 1 1]), [NaN NaN y(3:5)])
+%!assert (betapdf ([x, NaN], 1, 2), [y, NaN])
+
+%% Test class of input preserved
+%!assert (betapdf (single ([x, NaN]), 1, 2), single ([y, NaN]))
+%!assert (betapdf ([x, NaN], single (1), 2), single ([y, NaN]))
+%!assert (betapdf ([x, NaN], 1, single (2)), single ([y, NaN]))
+
+%% Beta (1/2,1/2) == arcsine distribution
+%!test
+%! x = rand (10,1);
+%! y = 1./(pi * sqrt (x.*(1-x)));
+%! assert (betapdf (x, 1/2, 1/2), y, 50*eps);
+
+%% Test large input values to betapdf
+%!assert (betapdf (0.5, 1000, 1000), 35.678, 1e-3)
+
+%% Test input validation
+%!error betapdf ()
+%!error betapdf (1)
+%!error betapdf (1,2)
+%!error betapdf (1,2,3,4)
+%!error betapdf (ones (3), ones (2), ones (2))
+%!error betapdf (ones (2), ones (3), ones (2))
+%!error betapdf (ones (2), ones (2), ones (3))
+%!error betapdf (i, 2, 2)
+%!error betapdf (2, i, 2)
+%!error betapdf (2, 2, i)
+
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/bland_altman.m
new/nan-3.5.2/inst/bland_altman.m
--- old/nan-3.5.0/inst/bland_altman.m 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/inst/bland_altman.m 2020-10-31 17:44:32.000000000 +0100
@@ -95,9 +95,9 @@
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.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);
@@ -117,5 +117,5 @@
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');
+ylabel('difference (m1-m2)');
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/gini.m new/nan-3.5.2/inst/gini.m
--- old/nan-3.5.0/inst/gini.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.5.2/inst/gini.m 2020-10-31 17:44:32.000000000 +0100
@@ -0,0 +1,35 @@
+function G = gini(data)
+% GINI computes the gini-coefficient [1] using by
+% computing the L-moments [2].
+%
+% USAGE:
+% G = gini(data)
+%
+%
+%
+% References:
+% [1] https://en.wikipedia.org/wiki/Gini_coefficient
+% [2] https://en.wikipedia.org/wiki/L-moment
+
+% Copyright (C) 2019,2020 by Alois Schlögl <[email protected]>
+% 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; see the file COPYING. If not, see
+%% <http://www.gnu.org/licenses/>.
+
+
+L = lmom(data,2);
+G = L(2)/L(1);
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/kappa.m new/nan-3.5.2/inst/kappa.m
--- old/nan-3.5.0/inst/kappa.m 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/inst/kappa.m 2020-10-31 17:44:32.000000000 +0100
@@ -37,10 +37,9 @@
% [5] http://ourworld.compuserve.com/homepages/jsuebersax/kappa.htm
% [6] http://en.wikipedia.org/wiki/Receiver_operating_characteristic
-% $Id$
-% Copyright (c) 1997-2006,2008,2009,2011 by Alois Schloegl
<[email protected]>
-% This function is part of the NaN-toolbox
-% http://pub.ist.ac.at/~schloegl/matlab/NaN/
+% Copyright (c) 1997-2020 by Alois Schloegl <[email protected]>
+% 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
@@ -184,6 +183,17 @@
X.Specificity = 1 - X.FPR;
X.Precision = X.PPV;
X.dprime = norminv(X.TPR) - norminv(X.FDR);
+
+ % statistical significance test of Matthews' correlation coefficient
+ NN = sum(H(:));
+ R = X.MCC;
+ R(isnan(R)) = 0;
+ tmp = 1 - R.*R;
+ tmp(tmp<0) = 0; % prevent tmp<0 i.e. imag(t)~=0
+ t = R.*sqrt(max(NN-2,0)./tmp)
+ sig = tcdf(t,NN-2);
+ sig = 2 * min(sig,1 - sig);
+ X.MCC_p_value = sig;
end;
kap = X;
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/lmom.m new/nan-3.5.2/inst/lmom.m
--- old/nan-3.5.0/inst/lmom.m 1970-01-01 01:00:00.000000000 +0100
+++ new/nan-3.5.2/inst/lmom.m 2020-10-31 17:44:32.000000000 +0100
@@ -0,0 +1,89 @@
+function LMOM = lmom(data,P,opt)
+% LMOM estimates the L-Moments [1,2] from a sample distribution
+% and might be a useful density estimation [1,3].
+% LMOM is equivalent to samlmo.F from dataplot [4].
+%
+% Usage:
+% XMOM = lmom(X,P)
+% XMOM = lmom(X,P,'ratios')
+%
+% X input data, NaN's are ignored
+% P maximum order, L moments 1:P are estimated
+% option: default 'false',
+% 'ratios': compute L-moment ratios
+% XMOM vector of L-Moments from 1:P
+% in case option='ratios', XMOM(3:P) will
+% return the L-moment rations (i.e. scaled L-moments).
+%
+% The current implementation is tested only on data sets up to 1000 samples
+% and P=10. The algorithm has not been analyzed with respect to accuracy and
+% computational efficiency. Eventually, this implementation should be
+% compared also to samlmu.F from dataplot [4], which is also used in [5].
+%
+% References:
+% [1] Hosking (1990), L-MOMENTS: ANALYSIS AND ESTIMATION OF DISTRIBUTIONS,
+% J. R. Statist. Soc. B (1990), 52,No. 1,pp. 105-124
+% [2] https://en.wikipedia.org/wiki/L-moment
+% [3] https://en.wikipedia.org/wiki/Density_estimation
+% [4] Hosking, function samlmo.F from https://github.com/usnistgov/dataplot
+% [5] 'lmom'-package for R, available from
+%
https://www.rdocumentation.org/packages/lmom/versions/2.8/topics/lmom-package
+
+% Copyright (C) 2019,2020 by Alois Schlögl <[email protected]>
+% 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; see the file COPYING. If not, see
+%% <http://www.gnu.org/licenses/>.
+
+
+if nargin<3
+ opt=0;
+end
+opt = strcmp(opt,'ratios');
+
+data(isnan(data))=[];
+F = [0:length(data)]'/length(data);
+u = sort(data);
+u = u([1,1:end]);
+
+% TODO: one might do this more efficiently
+p=repmat(NaN,P,P);
+for r = 1:P
+for k = 1:r
+ p(r,k)=bincoeff(r,k)*bincoeff(r+k,k)*(-1)^(r-k);
+end
+end
+
+for k = 1:P,
+ xi(k) = trapz(F, u .* F.^(k-1));
+ if k==1,
+ LMOM(k) = xi(k);
+ else
+ LMOM(k) = xi(1:k) * [(-1).^(k-1); p(k-1, 1:k-1)'];
+ end
+end
+if (opt && (P>2))
+ LMOM(3:P) = LMOM(3:P)/LMOM(2);
+end
+
+return
+
+% lambda(1) = trapz(F, [u] );
+% lambda(2) = trapz(F, [u] .* (2*F-1)) ;
+% lambda(3) = trapz(F, [u] .* (6*F.^2 - 6*F + 1)) ;
+% lambda(4) = trapz(F, [u] .* (20*F.^3 - 30*F.^2 + 12*F - 1)) ;
+%
+
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/load_fisheriris.m
new/nan-3.5.2/inst/load_fisheriris.m
--- old/nan-3.5.0/inst/load_fisheriris.m 2020-07-12 23:58:03.000000000
+0200
+++ new/nan-3.5.2/inst/load_fisheriris.m 2020-10-31 17:44:32.000000000
+0100
@@ -7,7 +7,7 @@
% [2] Duda,R.O., & Hart,P.E. (1973) Pattern Classification and Scene Analysis.
% (Q327.D83) John Wiley & Sons. ISBN 0-471-22361-1. See page 218.
-% Copyright (C) 2009,2010,2016,2019 by Alois Schloegl
<[email protected]>
+% Copyright (C) 2009,2010,2016,2019,2020 by Alois Schloegl
<[email protected]>
% This function is part of the NaN-toolbox
% http://pub.ist.ac.at/~schloegl/matlab/NaN/
@@ -27,31 +27,39 @@
if exist('OCTAVE_VERSION','builtin')
- if ~exist('iris.data','file')
- if strncmp(computer,'PCWIN',5)
- fprintf(1,'Download
http://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data and
save in local directory %s\nPress any key to continue ...\n',pwd);
+ IRIS=fullfile(tempdir(),'iris.dat');
+
+ if ~exist(IRIS,'file')
+ if exist('webread','file') % available in Octave 6 or 7
+ species =
webread('http://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data');
+ fid=fopen(IRIS,'w'); fwrite(fid,species,'char');
fclose(fid);
+ elseif strncmp(computer,'PCWIN',5) % on MXE-OCTAVE for
Windows, wget is available
+ fprintf(1,'Download
http://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data and
save in under %s\nPress any key to continue ...\n',IRIS);
else
- system('wget
http://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data');
+ system(['wget
http://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data -O
',IRIS]);
end;
end;
if exist('str2array','file')==3,
- tmp = fopen('iris.data');
species=fread(tmp,[1,inf],'uint8=>char'); fclose(tmp);
+ if ~exist('species','var')
+ tmp = fopen(IRIS);
species=fread(tmp,[1,inf],'uint8=>char'); fclose(tmp);
+ end
[meas, tmp, species] = str2array(species,',');
meas = meas(1:150, 1:4);
species = species(1:150, 5);
- elseif exist('OCTAVE_VERSION', 'builtin'),
- [a,b,c,d,species] = textread ('iris.data', '%f,%f,%f,%f,%s\n');
+ elseif exist('textread', 'file'),
+ [a,b,c,d,species] = textread (IRIS, '%f,%f,%f,%f,%s\n');
meas = [a,b,c,d];
+ clear a b c d;
if (size(meas,1)==151)
% remove empty line at the end
meas(151,:)=[];
species(151)=[];
end
else
- tmp = fopen('iris.data');
species=fread(tmp,[1,inf],'uint8=>char'); fclose(tmp);
- [meas,tmp,species]=str2double(species,',');
+ tmp = fopen(IRIS); species=fread(tmp,[1,inf],'uint8=>char');
fclose(tmp);
+ [meas,tmp,species]=str2double(species,',');
meas = meas(:,1:4);
species = species(:,5);
end
@@ -59,7 +67,7 @@
load fisheriris;
end;
-%!test
+%!xtest
%! load_fisheriris
%! assert(all(size(meas)==[150,4]))
%! assert(all(size(species)==[150,1]))
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/ttest.m new/nan-3.5.2/inst/ttest.m
--- old/nan-3.5.0/inst/ttest.m 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/inst/ttest.m 2020-10-31 17:44:32.000000000 +0100
@@ -146,7 +146,7 @@
end
%!test
-%! x = 8:0.1:12;
+%! x = [8:0.1:12,repmat(NaN,1,40)];
%! [h, pval, ci] = ttest (x, 10);
%! assert (h, 0)
%! assert (pval, 1, 10*eps)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.5.0/inst/xcovf.m new/nan-3.5.2/inst/xcovf.m
--- old/nan-3.5.0/inst/xcovf.m 2020-07-12 23:58:03.000000000 +0200
+++ new/nan-3.5.2/inst/xcovf.m 2020-10-31 17:44:32.000000000 +0100
@@ -24,7 +24,6 @@
%
% see also: COVM, XCORR
-% $Id$
% Copyright (C) 2005,2010,2011 by Alois Schloegl
<[email protected]>
% This function is part of the NaN-toolbox
% http://pub.ist.ac.at/~schloegl/matlab/NaN/
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