Hello community, here is the log from the commit of package octave-forge-statistics for openSUSE:Factory checked in at 2019-07-08 15:10:48 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/octave-forge-statistics (Old) and /work/SRC/openSUSE:Factory/.octave-forge-statistics.new.4615 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "octave-forge-statistics" Mon Jul 8 15:10:48 2019 rev:4 rq:713626 version:1.4.1 Changes: -------- --- /work/SRC/openSUSE:Factory/octave-forge-statistics/octave-forge-statistics.changes 2018-06-29 22:22:47.326646465 +0200 +++ /work/SRC/openSUSE:Factory/.octave-forge-statistics.new.4615/octave-forge-statistics.changes 2019-07-08 15:10:53.439337352 +0200 @@ -1,0 +2,18 @@ +Thu Jul 4 20:04:00 2019 UTC - hiwatari.seiji@gmail.com + +- Update to version 1.4.1: + * update install scripts for octave 5.0 depreciated functions + + * bug fixes to the following functions: + - pdist2.m: use max in distEucSq (Bug #50377) + - normpdf: use eps tolerance in tests (Bug #51963) + - fitgmdist: fix an output bug in fitgmdist + - t_test: Set tolerance on t_test BISTS (Bug #54557) + - gpXXXXX: change order of inputs to match matlab (Bug #54009) + - bartlett_test: df = k-1 (Bug #45894) + - gppdf: apply scale factor (Bug #54009) + - gmdistribution: updates for bug #54278, ##54279 + - wishrnd: Bug #55860 + - Add octave-bug-50365-Wrong-distance-results-from-kmeans-and-wrong-centers.patch + +------------------------------------------------------------------- Old: ---- statistics-1.4.0.tar.gz New: ---- octave-bug-50365-Wrong-distance-results-from-kmeans-and-wrong-centers.patch statistics-1.4.1.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ octave-forge-statistics.spec ++++++ --- /var/tmp/diff_new_pack.t4jadD/_old 2019-07-08 15:10:54.375338250 +0200 +++ /var/tmp/diff_new_pack.t4jadD/_new 2019-07-08 15:10:54.379338254 +0200 @@ -1,7 +1,7 @@ # # spec file for package octave-forge-statistics # -# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -12,19 +12,21 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # %define octpkg statistics Name: octave-forge-%{octpkg} -Version: 1.4.0 +Version: 1.4.1 Release: 0 Summary: Additional statistics functions for Octave License: GPL-3.0-or-later AND SUSE-Public-Domain Group: Productivity/Scientific/Math Url: http://octave.sourceforge.net Source0: http://downloads.sourceforge.net/octave/%{octpkg}-%{version}.tar.gz +# PATCH-FIX-UPSTREAM octave-bug-50365-Wrong-distance-results-from-kmeans-and-wrong-centers.patch https://savannah.gnu.org/bugs/?func=detailitem&item_id=50365 ajuanpi+dev@gmail.com -- fix bug #50365. Update distances and classes to best replica +Patch0: octave-bug-50365-Wrong-distance-results-from-kmeans-and-wrong-centers.patch BuildArch: noarch BuildRequires: octave-devel Requires: octave-cli >= 4.0.0 @@ -37,6 +39,7 @@ %prep %setup -q -c %{name}-%{version} %octave_pkg_src +%patch0 -p1 %build %octave_pkg_build ++++++ octave-bug-50365-Wrong-distance-results-from-kmeans-and-wrong-centers.patch ++++++ --- a/statistics-1.4.1/inst/kmeans.m +++ b/statistics-1.4.1/inst/kmeans.m @@ -143,9 +143,9 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) replicates_set_explicitly = false; ## Remove rows containing NaN / NA, but record which rows are used - data_idx = ! any (isnan (data), 2); + data_idx = ! any (isnan (data), 2); original_rows = rows (data); - data = data(data_idx,:); + data = data(data_idx,:); #used for getting the number of samples n_rows = rows (data); @@ -236,11 +236,14 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) if (isempty (k)) k = rows (start); elseif (rows (start) != k) - error ("kmeans: Number of initializers (%d) should match number of centroids (%d)", rows (start), k); + error (["kmeans: Number of initializers (%d) " ... + "should match number of centroids (%d)"], rows (start), k); endif if (replicates_set_explicitly) if (replicates != size (start, 3)) - error ("kmeans: The third dimension of the initializer (%d) should match the number of replicates (%d)", size (start, 3), replicates); + error (["kmeans: The third dimension of the initializer (%d) " ... + "should match the number of replicates (%d)"], ... + size (start, 3), replicates); endif else replicates = size (start, 3); @@ -251,32 +254,32 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) ## dist returns the distance btwn each row of matrix x and a row vector c switch (lower (distance)) case "sqeuclidean" - dist = @(x, c) (sumsq (bsxfun (@minus, x, c), 2)); - centroid = @(x) (mean (x,1)); + dist = @(x, c) sumsq (bsxfun (@minus, x, c), 2); + centroid = @(x) mean (x, 1); case "cityblock" - dist = @(x, c) (sum (abs (bsxfun (@minus, x, c)), 2)); - centroid = @(x) (median (x,1)); + dist = @(x, c) sum (abs (bsxfun (@minus, x, c)), 2); + centroid = @(x) median (x, 1); case "cosine" ## Pre-normalize all data. ## (when Octave implements normr, will use data = normr (data) ) for i = 1:rows (data) data(i,:) = data(i,:) / sqrt (sumsq (data(i,:))); endfor - dist = @(x, c) (1 - (x * c') ./ sqrt (sumsq (c))); - centroid = @(x) (mean (x,1)); ## already normalized + dist = @(x, c) 1 - (x * c') ./ sqrt (sumsq (c)); + centroid = @(x) mean (x, 1); ## already normalized case "correlation" - ## Pre-normalize all data. + ## Pre-normalize all data. data = data - mean (data, 2); - ## (when Octave implements normr, will use data = normr (data) ) + ## (when Octave implements normr, will use data = normr (data) ) for i = 1:rows (data) data(i,:) = data(i,:) / sqrt (sumsq (data(i,:))); endfor - - dist = @(x, c) (1 - (x * (c-mean (c))') ./ sqrt (sumsq (c-mean (c)))); - centroid = @(x) (mean (x,1)); ## already normalized + dist = @(x, c) 1 - (x * (c - mean (c))') ... + ./ sqrt (sumsq (c - mean (c))); + centroid = @(x) mean (x, 1); ## already normalized case "hamming" - dist = @(x, c) (sum (bsxfun (@ne, x, c), 2)); - centroid = @(x) (median (x,1)); + dist = @(x, c) sum (bsxfun (@ne, x, c), 2); + centroid = @(x) median (x, 1); otherwise error ("kmeans: unsupported distance parameter %s", distance); endswitch @@ -285,7 +288,6 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) ######################################## ## Now that k has been set (possibly by 'replicates' option), check/use it. - if (! isscalar (k)) error ("kmeans: second input argument must be a scalar"); endif @@ -293,27 +295,27 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) ## used to hold the distances from each sample to each class D = zeros (n_rows, k); - best = Inf; + best = Inf; best_centers = []; for rep = 1:replicates ## check for the 'start' property switch (lower (start)) case "sample" - idx = randperm (n_rows, k); + idx = randperm (n_rows, k); centers = data(idx, :); case "plus" # k-means++, by Arthur and Vassilios(?) centers(1,:) = data(randi (n_rows),:); - d = inf (n_rows, 1); # Distance to nearest centroid so far - for i = 2:k - d = min (d, dist (data, centers(i-1, :))); - centers(i,:) = data(find (cumsum (d) > rand * sum (d), 1), :); - endfor + d = inf (n_rows, 1); # Distance to nearest centroid so far + for i = 2:k + d = min (d, dist (data, centers(i - 1, :))); + centers(i,:) = data(find (cumsum (d) > rand * sum (d), 1), :); + endfor case "cluster" - idx = randperm (n_rows, max (k, ceil (n_rows/10))); - [~, centers] = kmeans (data(idx,:), k, "start", "sample", + idx = randperm (n_rows, max (k, ceil (n_rows / 10))); + [~, centers] = kmeans (data(idx,:), k, "start", "sample", ... "distance", distance); case "uniform" - # vectorised 'min_data + range .* rand' + # vectorised 'min_data + range .* rand' centers = bsxfun (@plus, min_data, bsxfun (@times, range, rand (k, columns (data)))); otherwise @@ -323,13 +325,9 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) ## Run the algorithm iter = 1; - ## Classify once before the loop; to set sumd, and if max_iter == 0 + ## Classify once before the loop; to set sumd, and if max_iter == 0 ## Compute distances and classify - for i = 1:k - D (:, i) = dist (data, centers(i, :)); - endfor - [~, classes] = min (D, [], 2); - sumd = obj_cost (D, classes); + [D, classes, sumd] = update_dist (data, centers, D, k, dist); while (err > 0.001 && iter++ <= max_iter) ## Calculate new centroids @@ -345,18 +343,18 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) ## farthest from any centroid (and not replacing an empty cluster ## from earlier in this pass) and add it to the empty cluster case 'singleton' - available = setdiff(1:n_rows, replaced_centroids); - [~, idx] = max (min (D(available,:)')); - idx = available(idx); + available = setdiff (1:n_rows, replaced_centroids); + [~, idx] = max (min (D(available,:)')); + idx = available(idx); replaced_centroids = [replaced_centroids, idx]; - classes(idx) = i; - membership(idx)=1; + classes(idx) = i; + membership(idx) = 1; ## if 'drop' then set C and D to NA case 'drop' centers(i,:) = NA; - D(i,:) = NA; + D(i,:) = NA; ## if 'error' then throw the error otherwise @@ -370,16 +368,9 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) endif endfor - ## Compute distances - for i = 1:k - D (:, i) = dist (data, centers(i, :)); - endfor - - ## Classify - [~, classes] = min (D, [], 2); - + ## Compute distances, classes and sums + [D, classes, new_sumd] = update_dist (data, centers, D, k, dist); ## calculate the difference in the sum of distances - new_sumd = obj_cost (D, classes); err = sum (sumd - new_sumd); ## update the current sum of distances sumd = new_sumd; @@ -390,22 +381,30 @@ function [classes, centers, sumd, D] = kmeans (data, k, varargin) endif endfor centers = best_centers; - sumd = best'; + ## Compute final distances, classes and sums + [D, classes, sumd] = update_dist (data, centers, D, k, dist); + + ## Return with equal size as inputs + if (original_rows != rows (data)) + final = NA (original_rows,1); + final(data_idx) = classes; ## other positions already NaN / NA + classes = final; + endif - final_classes = NA (original_rows,1); - final_classes(data_idx) = classes; ## other positions already NaN / NA - classes = final_classes; endfunction -## calculate the sum of within-class distances -function obj = obj_cost (D, classes) - obj = zeros (1,columns (D)); - for i = 1:columns (D) - idx = (classes == i); - obj(i) = sum (D(idx,i)); - end +## Update distances, classes and sums +function [D, classes, sumd] = update_dist (data, centers, D, k, dist) + for i = 1:k + D (:, i) = dist (data, centers(i, :)); + endfor + [~, classes] = min (D, [], 2); + ## calculate the sum of within-class distances + sumd = zeros (k, 1); + for i = 1:k + sumd(i) = sum (D(classes == i,i)); + endfor endfunction - ## Test input parsing %!error kmeans (rand (3,2), 4); ++++++ statistics-1.4.0.tar.gz -> statistics-1.4.1.tar.gz ++++++ ++++ 1623 lines of diff (skipped) ++++ retrying with extended exclude list diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/DESCRIPTION new/statistics-1.4.1/DESCRIPTION --- old/statistics-1.4.0/DESCRIPTION 2018-05-19 06:40:09.350499425 +0200 +++ new/statistics-1.4.1/DESCRIPTION 2019-03-17 14:45:17.000000000 +0100 @@ -1,6 +1,6 @@ Name: statistics -Version: 1.4.0 -Date: 2018-05-11 +Version: 1.4.1 +Date: 2019-03-17 Author: various authors Maintainer: Octave-Forge community <maintainers@octave.org> Title: Statistics diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/Makefile new/statistics-1.4.1/Makefile --- old/statistics-1.4.0/Makefile 2018-05-19 06:40:09.350499425 +0200 +++ new/statistics-1.4.1/Makefile 2019-03-17 14:45:17.000000000 +0100 @@ -2,11 +2,13 @@ ## Copyright 2015-2016 Oliver Heimlich ## Copyright 2017 Julien Bect <jbect@users.sf.net> ## Copyright 2017 Olaf Till <i7tiol@t-online.de> +## Copyright 2018 John Donoghue <john.donoghue@ieee.org> ## ## Copying and distribution of this file, with or without modification, ## are permitted in any medium without royalty provided the copyright ## notice and this notice are preserved. This file is offered as-is, ## without any warranty. +TOPDIR := $(shell pwd) ## Some basic tools (can be overriden using environment variables) SED ?= sed @@ -218,8 +220,7 @@ else __run_test_suite__ (dirs, {}); endif ' octave_test_commands = \ ' pkgs = pkg("list", "$(package)"); \ - cd ("$(target_dir)/"); \ - dirs = {sprintf(".installation/%s-%s", pkgs{1}.name, pkgs{1}.version)}; \ + dirs = {pkgs{1}.dir}; \ __run_test_suite__ (dirs, {}); ' ## the following works, too, but provides no overall summary output as ## __run_test_suite__ does: diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/NEWS new/statistics-1.4.1/NEWS --- old/statistics-1.4.0/NEWS 2018-05-19 06:40:09.354499405 +0200 +++ new/statistics-1.4.1/NEWS 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,18 @@ +Summary of important user-visible changes for statistics 1.4.1: +------------------------------------------------------------------- + ** update install scripts for octave 5.0 depreciated functions + + ** bug fixes to the following functions: + pdist2.m: use max in distEucSq (Bug #50377) + normpdf: use eps tolerance in tests (Bug #51963) + fitgmdist: fix an output bug in fitgmdist + t_test: Set tolerance on t_test BISTS (Bug #54557) + gpXXXXX: change order of inputs to match matlab (Bug #54009) + bartlett_test: df = k-1 (Bug #45894) + gppdf: apply scale factor (Bug #54009) + gmdistribution: updates for bug #54278, ##54279 + wishrnd: Bug #55860 + Summary of important user-visible changes for statistics 1.4.0: ------------------------------------------------------------------- @@ -8,12 +23,12 @@ gmdistribution sigma_pts - ** The following functions have been moved from the statisctics package but are - condtionally installed: + ** The following functions have been moved from the statistics package but are + conditionally installed: mad - ** The following functions have been moved from octave to be condtionally + ** The following functions have been moved from octave to be conditionally installed: BASE diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/PKG_ADD new/statistics-1.4.1/PKG_ADD --- old/statistics-1.4.0/PKG_ADD 2018-05-19 06:40:09.354499405 +0200 +++ new/statistics-1.4.1/PKG_ADD 2019-03-17 14:45:17.000000000 +0100 @@ -6,7 +6,14 @@ ## - PKG_ADD (and PKG_DEL?) is run during installation, too, from the ## root directory of the package, where no such subdirectories ## exist. -if (isdir (fullfile (fileparts (mfilename ("fullpath")), "base"))) - addpath (fullfile (fileparts (mfilename ("fullpath")), - {"base", "distributions", "models", "tests"}){:}); +if exist ("isfolder") == 0 + if (isdir (fullfile (fileparts (mfilename ("fullpath")), "base"))) + addpath (fullfile (fileparts (mfilename ("fullpath")), + {"base", "distributions", "models", "tests"}){:}); + endif +else + if (isfolder (fullfile (fileparts (mfilename ("fullpath")), "base"))) + addpath (fullfile (fileparts (mfilename ("fullpath")), + {"base", "distributions", "models", "tests"}){:}); + endif endif diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/PKG_DEL new/statistics-1.4.1/PKG_DEL --- old/statistics-1.4.0/PKG_DEL 2018-05-19 06:40:09.354499405 +0200 +++ new/statistics-1.4.1/PKG_DEL 2019-03-17 14:45:17.000000000 +0100 @@ -6,7 +6,14 @@ ## - PKG_ADD (and PKG_DEL?) is run during installation, too, from the ## root directory of the package, where no such subdirectories ## exist. -if (isdir (fullfile (fileparts (mfilename ("fullpath")), "base"))) - rmpath (fullfile (fileparts (mfilename ("fullpath")), +if exist ("isfolder") == 0 + if (isdir (fullfile (fileparts (mfilename ("fullpath")), "base"))) + rmpath (fullfile (fileparts (mfilename ("fullpath")), {"base", "distributions", "models", "tests"}){:}); + endif +else + if (isfolder (fullfile (fileparts (mfilename ("fullpath")), "base"))) + rmpath (fullfile (fileparts (mfilename ("fullpath")), + {"base", "distributions", "models", "tests"}){:}); + endif endif diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/bbscdf.m new/statistics-1.4.1/inst/bbscdf.m --- old/statistics-1.4.0/inst/bbscdf.m 2018-05-19 06:40:09.358499386 +0200 +++ new/statistics-1.4.1/inst/bbscdf.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1995-2015 Kurt Hornik ## @@ -18,7 +19,7 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} bbscdf (@var{x}, @var{location}, @var{scale}, @var{shape}) +## @deftypefn {} {} bbscdf (@var{x}, @var{shape}, @var{scale}, @var{location}) ## For each element of @var{x}, compute the cumulative distribution function ## (CDF) at @var{x} of the Birnbaum-Saunders distribution with parameters ## @var{location}, @var{scale} and @var{shape}. @@ -27,7 +28,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: CDF of the Birnbaum-Saunders distribution -function cdf = bbscdf (x, location, scale, shape) +function cdf = bbscdf (x, shape, scale, location) if (nargin != 4) print_usage (); @@ -74,21 +75,21 @@ %!shared x,y %! x = [-1, 0, 1, 2, Inf]; %! y = [0, 0, 1/2, 0.76024993890652337, 1]; -%!assert (bbscdf (x, zeros (1,5), ones (1,5), ones (1,5)), y, eps) -%!assert (bbscdf (x, zeros (1,5), 1, 1), y, eps) -%!assert (bbscdf (x, 0, ones (1,5), 1), y, eps) -%!assert (bbscdf (x, 0, 1, ones (1,5)), y, eps) -%!assert (bbscdf (x, 0, 1, 1), y, eps) -%!assert (bbscdf (x, [0, 0, NaN, 0, 0], 1, 1), [y(1:2), NaN, y(4:5)], eps) -%!assert (bbscdf (x, 0, [1, 1, NaN, 1, 1], 1), [y(1:2), NaN, y(4:5)], eps) -%!assert (bbscdf (x, 0, 1, [1, 1, NaN, 1, 1]), [y(1:2), NaN, y(4:5)], eps) -%!assert (bbscdf ([x, NaN], 0, 1, 1), [y, NaN], eps) +%!assert (bbscdf (x, ones (1,5), ones (1,5), zeros (1,5)), y, eps) +%!assert (bbscdf (x, 1, 1, zeros (1,5)), y, eps) +%!assert (bbscdf (x, 1, ones (1,5), 0), y, eps) +%!assert (bbscdf (x, ones (1,5), 1, 0), y, eps) +%!assert (bbscdf (x, 1, 1, 0), y, eps) +%!assert (bbscdf (x, 1, 1, [0, 0, NaN, 0, 0]), [y(1:2), NaN, y(4:5)], eps) +%!assert (bbscdf (x, 1, [1, 1, NaN, 1, 1], 0), [y(1:2), NaN, y(4:5)], eps) +%!assert (bbscdf (x, [1, 1, NaN, 1, 1], 1, 0), [y(1:2), NaN, y(4:5)], eps) +%!assert (bbscdf ([x, NaN], 1, 1, 0), [y, NaN], eps) ## Test class of input preserved -%!assert (bbscdf (single ([x, NaN]), 0, 1, 1), single ([y, NaN]), eps('single')) -%!assert (bbscdf ([x, NaN], single (0), 1, 1), single ([y, NaN]), eps('single')) -%!assert (bbscdf ([x, NaN], 0, single (1), 1), single ([y, NaN]), eps('single')) -%!assert (bbscdf ([x, NaN], 0, 1, single (1)), single ([y, NaN]), eps('single')) +%!assert (bbscdf (single ([x, NaN]), 1, 1, 0), single ([y, NaN]), eps('single')) +%!assert (bbscdf ([x, NaN], 1, 1, single (0)), single ([y, NaN]), eps('single')) +%!assert (bbscdf ([x, NaN], 1, single (1), 0), single ([y, NaN]), eps('single')) +%!assert (bbscdf ([x, NaN], single (1), 1, 0), single ([y, NaN]), eps('single')) ## Test input validation %!error bbscdf () @@ -99,8 +100,8 @@ %!error bbscdf (ones (2), ones (3), ones(2), ones(2)) %!error bbscdf (ones (2), ones (2), ones(3), ones(2)) %!error bbscdf (ones (2), ones (2), ones(2), ones(3)) -%!error bbscdf (i, 2, 3, 4) -%!error bbscdf (1, i, 3, 4) -%!error bbscdf (1, 2, i, 4) -%!error bbscdf (1, 2, 3, i) +%!error bbscdf (i, 4, 3, 2) +%!error bbscdf (1, i, 3, 2) +%!error bbscdf (1, 4, i, 2) +%!error bbscdf (1, 4, 3, i) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/bbsinv.m new/statistics-1.4.1/inst/bbsinv.m --- old/statistics-1.4.0/inst/bbsinv.m 2018-05-19 06:40:09.358499386 +0200 +++ new/statistics-1.4.1/inst/bbsinv.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1995-2015 Kurt Hornik ## @@ -18,7 +19,7 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} bbsinv (@var{x}, @var{location}, @var{scale}, @var{shape}) +## @deftypefn {} {} bbsinv (@var{x}, @var{shape}, @var{scale}, @var{location}) ## For each element of @var{x}, compute the quantile (the inverse of the CDF) ## at @var{x} of the Birnbaum-Saunders distribution with parameters ## @var{location}, @var{scale}, and @var{shape}. @@ -27,7 +28,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: Quantile function of the Birnbaum-Saunders distribution -function inv = bbsinv (x, location, scale, shape) +function inv = bbsinv (x, shape, scale, location) if (nargin != 4) print_usage (); @@ -82,21 +83,21 @@ %! f = @(x,a,b,c) (a + b * (c * norminv (x) + sqrt (4 + (c * norminv(x))^2))^2) / 4; %! x = [-1, 0, 1/4, 1/2, 1, 2]; %! y = [0, 0, f(1/4, 0, 1, 1), 1, Inf, NaN]; -%!assert (bbsinv (x, zeros (1,6), ones (1,6), ones (1,6)), y) -%!assert (bbsinv (x, zeros (1,6), 1, 1), y) -%!assert (bbsinv (x, 0, ones (1,6), 1), y) -%!assert (bbsinv (x, 0, 1, ones (1,6)), y) -%!assert (bbsinv (x, 0, 1, 1), y) -%!assert (bbsinv (x, [0, 0, 0, NaN, 0, 0], 1, 1), [y(1:3), NaN, y(5:6)]) -%!assert (bbsinv (x, 0, [1, 1, 1, NaN, 1, 1], 1), [y(1:3), NaN, y(5:6)]) -%!assert (bbsinv (x, 0, 1, [1, 1, 1, NaN, 1, 1]), [y(1:3), NaN, y(5:6)]) -%!assert (bbsinv ([x, NaN], 0, 1, 1), [y, NaN]) +%!assert (bbsinv (x, ones (1,6), ones (1,6), zeros (1,6)), y) +%!assert (bbsinv (x, 1, 1, zeros (1,6)), y) +%!assert (bbsinv (x, 1, ones (1,6), 0), y) +%!assert (bbsinv (x, ones (1,6), 1, 0), y) +%!assert (bbsinv (x, 1, 1, 0), y) +%!assert (bbsinv (x, 1, 1, [0, 0, 0, NaN, 0, 0]), [y(1:3), NaN, y(5:6)]) +%!assert (bbsinv (x, 1, [1, 1, 1, NaN, 1, 1], 0), [y(1:3), NaN, y(5:6)]) +%!assert (bbsinv (x, [1, 1, 1, NaN, 1, 1], 1, 0), [y(1:3), NaN, y(5:6)]) +%!assert (bbsinv ([x, NaN], 1, 1, 0), [y, NaN]) ## Test class of input preserved -%!assert (bbsinv (single ([x, NaN]), 0, 1, 1), single ([y, NaN])) -%!assert (bbsinv ([x, NaN], single (0), 1, 1), single ([y, NaN])) -%!assert (bbsinv ([x, NaN], 0, single (1), 1), single ([y, NaN])) -%!assert (bbsinv ([x, NaN], 0, 1, single (1)), single ([y, NaN])) +%!assert (bbsinv (single ([x, NaN]), 1, 1, 0), single ([y, NaN])) +%!assert (bbsinv ([x, NaN], 1, 1, single (0)), single ([y, NaN])) +%!assert (bbsinv ([x, NaN], 1, single (1), 0), single ([y, NaN])) +%!assert (bbsinv ([x, NaN], single (1), 1, 0), single ([y, NaN])) ## Test input validation %!error bbsinv () @@ -107,8 +108,8 @@ %!error bbsinv (ones (2), ones (3), ones(2), ones(2)) %!error bbsinv (ones (2), ones (2), ones(3), ones(2)) %!error bbsinv (ones (2), ones (2), ones(2), ones(3)) -%!error bbsinv (i, 2, 3, 4) -%!error bbsinv (1, i, 3, 4) -%!error bbsinv (1, 2, i, 4) -%!error bbsinv (1, 2, 3, i) +%!error bbsinv (i, 4, 3, 2) +%!error bbsinv (1, i, 3, 2) +%!error bbsinv (1, 4, i, 2) +%!error bbsinv (1, 4, 3, i) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/bbspdf.m new/statistics-1.4.1/inst/bbspdf.m --- old/statistics-1.4.0/inst/bbspdf.m 2018-05-19 06:40:09.358499386 +0200 +++ new/statistics-1.4.1/inst/bbspdf.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1995-2015 Kurt Hornik ## @@ -18,7 +19,7 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} bbspdf (@var{x}, @var{location}, @var{scale}, @var{shape}) +## @deftypefn {} {} bbspdf (@var{x}, @var{shape}, @var{scale}, @var{location}) ## For each element of @var{x}, compute the probability density function (PDF) ## at @var{x} of the Birnbaum-Saunders distribution with parameters ## @var{location}, @var{scale} and @var{shape}. @@ -27,7 +28,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: PDF of the Birnbaum-Saunders distribution -function pdf = bbspdf (x, location, scale, shape) +function pdf = bbspdf (x, shape, scale, location) if (nargin != 4) print_usage (); @@ -80,21 +81,21 @@ %!shared x,y %! x = [-1, 0, 1, 2, Inf]; %! y = [0, 0, 0.3989422804014327, 0.1647717335503959, 0]; -%!assert (bbspdf (x, zeros (1,5), ones (1,5), ones (1,5)), y, eps) -%!assert (bbspdf (x, zeros (1,5), 1, 1), y, eps) -%!assert (bbspdf (x, 0, ones (1,5), 1), y, eps) -%!assert (bbspdf (x, 0, 1, ones (1,5)), y, eps) -%!assert (bbspdf (x, 0, 1, 1), y, eps) -%!assert (bbspdf (x, [0, 0, NaN, 0, 0], 1, 1), [y(1:2), NaN, y(4:5)], eps) -%!assert (bbspdf (x, 0, [1, 1, NaN, 1, 1], 1), [y(1:2), NaN, y(4:5)], eps) -%!assert (bbspdf (x, 0, 1, [1, 1, NaN, 1, 1]), [y(1:2), NaN, y(4:5)], eps) -%!assert (bbspdf ([x, NaN], 0, 1, 1), [y, NaN], eps) +%!assert (bbspdf (x, ones (1,5), ones (1,5), zeros (1,5)), y, eps) +%!assert (bbspdf (x, 1, 1, zeros (1,5)), y, eps) +%!assert (bbspdf (x, 1, ones (1,5), 0), y, eps) +%!assert (bbspdf (x, ones (1,5), 1, 0), y, eps) +%!assert (bbspdf (x, 1, 1, 0), y, eps) +%!assert (bbspdf (x, 1, 1, [0, 0, NaN, 0, 0]), [y(1:2), NaN, y(4:5)], eps) +%!assert (bbspdf (x, 1, [1, 1, NaN, 1, 1], 0), [y(1:2), NaN, y(4:5)], eps) +%!assert (bbspdf (x, [1, 1, NaN, 1, 1], 1, 0), [y(1:2), NaN, y(4:5)], eps) +%!assert (bbspdf ([x, NaN], 1, 1, 0), [y, NaN], eps) ## Test class of input preserved -%!assert (bbspdf (single ([x, NaN]), 0, 1, 1), single ([y, NaN]), eps('single')) -%!assert (bbspdf ([x, NaN], single (0), 1, 1), single ([y, NaN]), eps('single')) -%!assert (bbspdf ([x, NaN], 0, single (1), 1), single ([y, NaN]), eps('single')) -%!assert (bbspdf ([x, NaN], 0, 1, single (1)), single ([y, NaN]), eps('single')) +%!assert (bbspdf (single ([x, NaN]), 1, 1, 0), single ([y, NaN]), eps('single')) +%!assert (bbspdf ([x, NaN], 1, 1, single (0)), single ([y, NaN]), eps('single')) +%!assert (bbspdf ([x, NaN], 1, single (1), 0), single ([y, NaN]), eps('single')) +%!assert (bbspdf ([x, NaN], single (1), 1, 0), single ([y, NaN]), eps('single')) ## Test input validation %!error bbspdf () @@ -105,8 +106,8 @@ %!error bbspdf (ones (2), ones (3), ones(2), ones(2)) %!error bbspdf (ones (2), ones (2), ones(3), ones(2)) %!error bbspdf (ones (2), ones (2), ones(2), ones(3)) -%!error bbspdf (i, 2, 3, 4) -%!error bbspdf (1, i, 3, 4) -%!error bbspdf (1, 2, i, 4) -%!error bbspdf (1, 2, 3, i) +%!error bbspdf (i, 4, 3, 2) +%!error bbspdf (1, i, 3, 2) +%!error bbspdf (1, 4, i, 2) +%!error bbspdf (1, 4, 3, i) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/bbsrnd.m new/statistics-1.4.1/inst/bbsrnd.m --- old/statistics-1.4.0/inst/bbsrnd.m 2018-05-19 06:40:09.358499386 +0200 +++ new/statistics-1.4.1/inst/bbsrnd.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1995-2015 Kurt Hornik ## @@ -18,10 +19,10 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} bbsrnd (@var{location}, @var{scale}, @var{shape}) -## @deftypefnx {} {} bbsrnd (@var{location}, @var{scale}, @var{shape}, @var{r}) -## @deftypefnx {} {} bbsrnd (@var{location}, @var{scale}, @var{shape}, @var{r}, @var{c}, @dots{}) -## @deftypefnx {} {} bbsrnd (@var{location}, @var{scale}, @var{shape}, [@var{sz}]) +## @deftypefn {} {} bbsrnd (@var{shape}, @var{scale}, @var{location}) +## @deftypefnx {} {} bbsrnd (@var{shape}, @var{scale}, @var{location}, @var{r}) +## @deftypefnx {} {} bbsrnd (@var{shape}, @var{scale}, @var{location}, @var{r}, @var{c}, @dots{}) +## @deftypefnx {} {} bbsrnd (@var{shape}, @var{scale}, @var{location}, [@var{sz}]) ## Return a matrix of random samples from the Birnbaum-Saunders ## distribution with parameters @var{location}, @var{scale} and @var{shape}. ## @@ -38,7 +39,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: Random deviates from the Birnbaum-Saunders distribution -function rnd = bbsrnd (location, scale, shape, varargin) +function rnd = bbsrnd (shape, scale, location, varargin) if (nargin < 3) print_usage (); @@ -105,25 +106,25 @@ endfunction -%!assert (size (bbsrnd (0, 1, 1)), [1 1]) -%!assert (size (bbsrnd (zeros (2,1), 1, 1)), [2, 1]) -%!assert (size (bbsrnd (zeros (2,2), 1, 1)), [2, 2]) -%!assert (size (bbsrnd (0, ones (2,1), 1)), [2, 1]) -%!assert (size (bbsrnd (0, ones (2,2), 1)), [2, 2]) -%!assert (size (bbsrnd (0, 1, ones (2,1))), [2, 1]) -%!assert (size (bbsrnd (0, 1, ones (2,2))), [2, 2]) -%!assert (size (bbsrnd (0, 1, 1, 3)), [3, 3]) -%!assert (size (bbsrnd (0, 1, 1, [4 1])), [4, 1]) -%!assert (size (bbsrnd (0, 1, 1, 4, 1)), [4, 1]) +%!assert (size (bbsrnd (1, 1, 0)), [1 1]) +%!assert (size (bbsrnd (1, 1, zeros (2,1))), [2, 1]) +%!assert (size (bbsrnd (1, 1, zeros (2,2))), [2, 2]) +%!assert (size (bbsrnd (1, ones (2,1), 0)), [2, 1]) +%!assert (size (bbsrnd (1, ones (2,2), 0)), [2, 2]) +%!assert (size (bbsrnd (ones (2,1), 1, 0)), [2, 1]) +%!assert (size (bbsrnd (ones (2,2), 1, 0)), [2, 2]) +%!assert (size (bbsrnd (1, 1, 0, 3)), [3, 3]) +%!assert (size (bbsrnd (1, 1, 0, [4 1])), [4, 1]) +%!assert (size (bbsrnd (1, 1, 0, 4, 1)), [4, 1]) ## Test class of input preserved -%!assert (class (bbsrnd (0,1,1)), "double") -%!assert (class (bbsrnd (single (0),1,1)), "single") -%!assert (class (bbsrnd (single ([0 0]),1,1)), "single") -%!assert (class (bbsrnd (0,single (1),1)), "single") -%!assert (class (bbsrnd (0,single ([1 1]),1)), "single") -%!assert (class (bbsrnd (0,1,single (1))), "single") -%!assert (class (bbsrnd (0,1,single ([1 1]))), "single") +%!assert (class (bbsrnd (1,1,0)), "double") +%!assert (class (bbsrnd (1, 1, single (0))), "single") +%!assert (class (bbsrnd (1, 1, single ([0 0]))), "single") +%!assert (class (bbsrnd (1, single (1), 0)), "single") +%!assert (class (bbsrnd (1, single ([1 1]), 0)), "single") +%!assert (class (bbsrnd (single (1), 1, 0)), "single") +%!assert (class (bbsrnd (single ([1 1]), 1, 0)), "single") ## Test input validation %!error bbsrnd () @@ -138,7 +139,7 @@ %!error bbsrnd (1,2,3, -1) %!error bbsrnd (1,2,3, ones (2)) %!error bbsrnd (1,2,3, [2 -1 2]) -%!error bbsrnd (ones (2),1,2, 3) -%!error bbsrnd (ones (2),1,2, [3, 2]) -%!error bbsrnd (ones (2),1,2, 3, 2) +%!error bbsrnd (2, 1, ones (2), 3) +%!error bbsrnd (2, 1, ones (2), [3, 2]) +%!error bbsrnd (2, 1, ones (2), 3, 2) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/fitgmdist.m new/statistics-1.4.1/inst/fitgmdist.m --- old/statistics-1.4.0/inst/fitgmdist.m 2018-05-19 06:40:09.370499328 +0200 +++ new/statistics-1.4.1/inst/fitgmdist.m 2019-03-17 14:45:17.000000000 +0100 @@ -511,7 +511,7 @@ obj = gmdistribution (best_params.mu, best_params.Sigma, best_params.p'); if (Display == 1) fprintf (" %d iterations log-likelihood = %g\n", ... - -extra.NegativeLogLikelihood, extra.NumIterations); + extra.NumIterations, -extra.NegativeLogLikelihood); endif endfunction diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/gmdistribution.m new/statistics-1.4.1/inst/gmdistribution.m --- old/statistics-1.4.0/inst/gmdistribution.m 2018-05-19 06:40:09.374499307 +0200 +++ new/statistics-1.4.1/inst/gmdistribution.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,5 @@ ## Copyright (C) 2015 Lachlan Andrew <lachlanbis@gmail.com> +## Copyright (C) 2018 John Donoghue <john.donoghue@ieee.org> ## ## 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 @@ -229,8 +230,11 @@ ######################################## ## Random numbers from Gaussian mixture distribution function c = random (obj,n) + if nargin == 1 + n = 1; + endif c = zeros (n, obj.NumVariables); - classes = randsample (obj.NumVariables, n, true, obj.ComponentProportion); + classes = randsample (obj.NumComponents, n, true, obj.ComponentProportion); if (obj.SharedCovariance) if (obj.DiagonalCovariance) sig = diag (obj.Sigma); @@ -262,7 +266,7 @@ methods (Static) ## Gaussian mixture parameter estimates function c = fit (X,k,varargin) - c = fitgmdist (X,k,varargin); + c = fitgmdist (X,k,varargin{:}); endfunction endmethods @@ -338,4 +342,7 @@ %! %! R = GM.random(20); %! assert (size(R), [20, 2]); +%! +%! R = GM.random(); +%! assert (size(R), [1, 2]); diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/gpcdf.m new/statistics-1.4.1/inst/gpcdf.m --- old/statistics-1.4.0/inst/gpcdf.m 2018-05-19 06:40:09.374499307 +0200 +++ new/statistics-1.4.1/inst/gpcdf.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1997-2015 Kurt Hornik ## @@ -18,7 +19,7 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} gpcdf (@var{x}, @var{location}, @var{scale}, @var{shape}) +## @deftypefn {} {} gpcdf (@var{x}, @var{shape}, @var{scale}, @var{location}) ## Compute the cumulative distribution function (CDF) at @var{x} of the ## generalized Pareto distribution with parameters @var{location}, @var{scale}, ## and @var{shape}. @@ -27,7 +28,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: PDF of the generalized Pareto distribution -function cdf = gpcdf (x, location, scale, shape) +function cdf = gpcdf (x, shape, scale, location) if (nargin != 4) print_usage (); @@ -113,50 +114,50 @@ %! y3 = [0, 0, 0, 1/2, 1, 1]; %! seps = eps('single')*5; %!assert (gpcdf (x, zeros (1,6), ones (1,6), zeros (1,6)), y1, eps) -%!assert (gpcdf (x, zeros (1,6), 1, 0), y1, eps) -%!assert (gpcdf (x, 0, ones (1,6), 0), y1, eps) %!assert (gpcdf (x, 0, 1, zeros (1,6)), y1, eps) +%!assert (gpcdf (x, 0, ones (1,6), 0), y1, eps) +%!assert (gpcdf (x, zeros (1,6), 1, 0), y1, eps) %!assert (gpcdf (x, 0, 1, 0), y1, eps) -%!assert (gpcdf (x, [0, 0, 0, NaN, 0, 0], 1, 0), [y1(1:3), NaN, y1(5:6)], eps) -%!assert (gpcdf (x, 0, [1, 1, 1, NaN, 1, 1], 0), [y1(1:3), NaN, y1(5:6)], eps) %!assert (gpcdf (x, 0, 1, [0, 0, 0, NaN, 0, 0]), [y1(1:3), NaN, y1(5:6)], eps) +%!assert (gpcdf (x, 0, [1, 1, 1, NaN, 1, 1], 0), [y1(1:3), NaN, y1(5:6)], eps) +%!assert (gpcdf (x, [0, 0, 0, NaN, 0, 0], 1, 0), [y1(1:3), NaN, y1(5:6)], eps) %!assert (gpcdf ([x(1:3), NaN, x(5:6)], 0, 1, 0), [y1(1:3), NaN, y1(5:6)], eps) -%!assert (gpcdf (x, zeros (1,6), ones (1,6), ones (1,6)), y2, eps) -%!assert (gpcdf (x, zeros (1,6), 1, 1), y2, eps) -%!assert (gpcdf (x, 0, ones (1,6), 1), y2, eps) -%!assert (gpcdf (x, 0, 1, ones (1,6)), y2, eps) -%!assert (gpcdf (x, 0, 1, 1), y2, eps) -%!assert (gpcdf (x, [0, 0, 0, NaN, 0, 0], 1, 1), [y2(1:3), NaN, y2(5:6)], eps) -%!assert (gpcdf (x, 0, [1, 1, 1, NaN, 1, 1], 1), [y2(1:3), NaN, y2(5:6)], eps) -%!assert (gpcdf (x, 0, 1, [1, 1, 1, NaN, 1, 1]), [y2(1:3), NaN, y2(5:6)], eps) -%!assert (gpcdf ([x(1:3), NaN, x(5:6)], 0, 1, 1), [y2(1:3), NaN, y2(5:6)], eps) - -%!assert (gpcdf (x, zeros (1,6), ones (1,6), -ones (1,6)), y3, eps) -%!assert (gpcdf (x, zeros (1,6), 1, -1), y3, eps) -%!assert (gpcdf (x, 0, ones (1,6), -1), y3, eps) -%!assert (gpcdf (x, 0, 1, -ones (1,6)), y3, eps) -%!assert (gpcdf (x, 0, 1, -1), y3, eps) -%!assert (gpcdf (x, [0, 0, 0, NaN, 0, 0], 1, -1), [y1(1:3), NaN, y3(5:6)], eps) -%!assert (gpcdf (x, 0, [1, 1, 1, NaN, 1, 1], -1), [y1(1:3), NaN, y3(5:6)], eps) -%!assert (gpcdf (x, 0, 1, [-1, -1, -1, NaN, -1, -1]), [y1(1:3), NaN, y3(5:6)], eps) -%!assert (gpcdf ([x(1:3), NaN, x(5:6)], 0, 1, -1), [y1(1:3), NaN, y3(5:6)], eps) +%!assert (gpcdf (x, ones (1,6), ones (1,6), zeros (1,6)), y2, eps) +%!assert (gpcdf (x, 1, 1, zeros (1,6)), y2, eps) +%!assert (gpcdf (x, 1, ones (1,6), 0), y2, eps) +%!assert (gpcdf (x, ones (1,6), 1, 0), y2, eps) +%!assert (gpcdf (x, 1, 1, 0), y2, eps) +%!assert (gpcdf (x, 1, 1, [0, 0, 0, NaN, 0, 0]), [y2(1:3), NaN, y2(5:6)], eps) +%!assert (gpcdf (x, 1, [1, 1, 1, NaN, 1, 1], 0), [y2(1:3), NaN, y2(5:6)], eps) +%!assert (gpcdf (x, [1, 1, 1, NaN, 1, 1], 1, 0), [y2(1:3), NaN, y2(5:6)], eps) +%!assert (gpcdf ([x(1:3), NaN, x(5:6)], 1, 1, 0), [y2(1:3), NaN, y2(5:6)], eps) + +%!assert (gpcdf (x, -ones (1,6), ones (1,6), zeros (1,6)), y3, eps) +%!assert (gpcdf (x, -1, 1, zeros (1,6)), y3, eps) +%!assert (gpcdf (x, -1, ones (1,6), 0), y3, eps) +%!assert (gpcdf (x, -ones (1,6), 1, 0), y3, eps) +%!assert (gpcdf (x, -1, 1, 0), y3, eps) +%!assert (gpcdf (x, -1, 1, [0, 0, 0, NaN, 0, 0]), [y1(1:3), NaN, y3(5:6)], eps) +%!assert (gpcdf (x, -1, [1, 1, 1, NaN, 1, 1], 0), [y1(1:3), NaN, y3(5:6)], eps) +%!assert (gpcdf (x, [-1, -1, -1, NaN, -1, -1], 1, 0), [y1(1:3), NaN, y3(5:6)], eps) +%!assert (gpcdf ([x(1:3), NaN, x(5:6)], -1, 1, 0), [y1(1:3), NaN, y3(5:6)], eps) ## Test class of input preserved %!assert (gpcdf (single ([x, NaN]), 0, 1, 0), single ([y1, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], single (0), 1, 0), single ([y1, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], 0, single (1), 0), single ([y1, NaN]), eps('single')) %!assert (gpcdf ([x, NaN], 0, 1, single (0)), single ([y1, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], 0, single (1), 0), single ([y1, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], single (0), 1, 0), single ([y1, NaN]), eps('single')) -%!assert (gpcdf (single ([x, NaN]), 0, 1, 1), single ([y2, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], single (0), 1, 1), single ([y2, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], 0, single (1), 1), single ([y2, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], 0, 1, single (1)), single ([y2, NaN]), eps('single')) - -%!assert (gpcdf (single ([x, NaN]), 0, 1, -1), single ([y3, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], single (0), 1, -1), single ([y3, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], 0, single (1), -1), single ([y3, NaN]), eps('single')) -%!assert (gpcdf ([x, NaN], 0, 1, single (-1)), single ([y3, NaN]), eps('single')) +%!assert (gpcdf (single ([x, NaN]), 1, 1, 0), single ([y2, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], 1, 1, single (0)), single ([y2, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], 1, single (1), 0), single ([y2, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], single (1), 1, 0), single ([y2, NaN]), eps('single')) + +%!assert (gpcdf (single ([x, NaN]), -1, 1, 0), single ([y3, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], -1, 1, single (0)), single ([y3, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], -1, single (1), 0), single ([y3, NaN]), eps('single')) +%!assert (gpcdf ([x, NaN], single (-1), 1, 0), single ([y3, NaN]), eps('single')) ## Test input validation %!error gpcdf () @@ -165,9 +166,9 @@ %!error gpcdf (1,2,3) %!error gpcdf (1,2,3,4,5) %!error gpcdf (ones (3), ones (2), ones (2), ones (2)) -%!error gpcdf (ones (2), ones (3), ones (2), ones (2)) -%!error gpcdf (ones (2), ones (2), ones (3), ones (2)) %!error gpcdf (ones (2), ones (2), ones (2), ones (3)) +%!error gpcdf (ones (2), ones (2), ones (3), ones (2)) +%!error gpcdf (ones (2), ones (3), ones (2), ones (2)) %!error gpcdf (i, 2, 2, 2) %!error gpcdf (2, i, 2, 2) %!error gpcdf (2, 2, i, 2) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/gpinv.m new/statistics-1.4.1/inst/gpinv.m --- old/statistics-1.4.0/inst/gpinv.m 2018-05-19 06:40:09.374499307 +0200 +++ new/statistics-1.4.1/inst/gpinv.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1997-2015 Kurt Hornik ## @@ -18,7 +19,7 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} gpinv (@var{x}, @var{location}, @var{scale}, @var{shape}) +## @deftypefn {} {} gpinv (@var{x}, @var{shape}, @var{scale}, @var{location}) ## For each element of @var{x}, compute the quantile (the inverse of the CDF) ## at @var{x} of the generalized Pareto distribution with parameters ## @var{location}, @var{scale}, and @var{shape}. @@ -27,7 +28,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: Quantile function of the generalized Pareto distribution -function inv = gpinv (x, location, scale, shape) +function inv = gpinv (x, shape, scale, location) if (nargin != 4) print_usage (); endif @@ -99,50 +100,50 @@ %! y2 = [NaN, 0, 1, Inf, NaN]; %! y3 = [NaN, 0, 1/2, 1, NaN]; %!assert (gpinv (x, zeros (1,5), ones (1,5), zeros (1,5)), y1) -%!assert (gpinv (x, zeros (1,5), 1, 0), y1) -%!assert (gpinv (x, 0, ones (1,5), 0), y1) %!assert (gpinv (x, 0, 1, zeros (1,5)), y1) +%!assert (gpinv (x, 0, ones (1,5), 0), y1) +%!assert (gpinv (x, zeros (1,5), 1, 0), y1) %!assert (gpinv (x, 0, 1, 0), y1) -%!assert (gpinv (x, [0, 0, NaN, 0, 0], 1, 0), [y1(1:2), NaN, y1(4:5)]) -%!assert (gpinv (x, 0, [1, 1, NaN, 1, 1], 0), [y1(1:2), NaN, y1(4:5)]) %!assert (gpinv (x, 0, 1, [0, 0, NaN, 0, 0]), [y1(1:2), NaN, y1(4:5)]) +%!assert (gpinv (x, 0, [1, 1, NaN, 1, 1], 0), [y1(1:2), NaN, y1(4:5)]) +%!assert (gpinv (x, [0, 0, NaN, 0, 0], 1, 0), [y1(1:2), NaN, y1(4:5)]) %!assert (gpinv ([x(1:2), NaN, x(4:5)], 0, 1, 0), [y1(1:2), NaN, y1(4:5)]) -%!assert (gpinv (x, zeros (1,5), ones (1,5), ones (1,5)), y2) -%!assert (gpinv (x, zeros (1,5), 1, 1), y2) -%!assert (gpinv (x, 0, ones (1,5), 1), y2) -%!assert (gpinv (x, 0, 1, ones (1,5)), y2) -%!assert (gpinv (x, 0, 1, 1), y2) -%!assert (gpinv (x, [0, 0, NaN, 0, 0], 1, 1), [y2(1:2), NaN, y2(4:5)]) -%!assert (gpinv (x, 0, [1, 1, NaN, 1, 1], 1), [y2(1:2), NaN, y2(4:5)]) -%!assert (gpinv (x, 0, 1, [1, 1, NaN, 1, 1]), [y2(1:2), NaN, y2(4:5)]) -%!assert (gpinv ([x(1:2), NaN, x(4:5)], 0, 1, 1), [y2(1:2), NaN, y2(4:5)]) - -%!assert (gpinv (x, zeros (1,5), ones (1,5), -ones (1,5)), y3) -%!assert (gpinv (x, zeros (1,5), 1, -1), y3) -%!assert (gpinv (x, 0, ones (1,5), -1), y3) -%!assert (gpinv (x, 0, 1, -ones (1,5)), y3) -%!assert (gpinv (x, 0, 1, -1), y3) -%!assert (gpinv (x, [0, 0, NaN, 0, 0], 1, -1), [y3(1:2), NaN, y3(4:5)]) -%!assert (gpinv (x, 0, [1, 1, NaN, 1, 1], -1), [y3(1:2), NaN, y3(4:5)]) -%!assert (gpinv (x, 0, 1, -[1, 1, NaN, 1, 1]), [y3(1:2), NaN, y3(4:5)]) -%!assert (gpinv ([x(1:2), NaN, x(4:5)], 0, 1, -1), [y3(1:2), NaN, y3(4:5)]) +%!assert (gpinv (x, ones (1,5), ones (1,5), zeros (1,5)), y2) +%!assert (gpinv (x, 1, 1, zeros (1,5)), y2) +%!assert (gpinv (x, 1, ones (1,5), 0), y2) +%!assert (gpinv (x, ones (1,5), 1, 0), y2) +%!assert (gpinv (x, 1, 1, 0), y2) +%!assert (gpinv (x, 1, 1, [0, 0, NaN, 0, 0]), [y2(1:2), NaN, y2(4:5)]) +%!assert (gpinv (x, 1, [1, 1, NaN, 1, 1], 0), [y2(1:2), NaN, y2(4:5)]) +%!assert (gpinv (x, [1, 1, NaN, 1, 1], 1, 0), [y2(1:2), NaN, y2(4:5)]) +%!assert (gpinv ([x(1:2), NaN, x(4:5)], 1, 1, 0), [y2(1:2), NaN, y2(4:5)]) + +%!assert (gpinv (x, -ones (1,5), ones (1,5), zeros (1,5)), y3) +%!assert (gpinv (x, -1, 1, zeros (1,5)), y3) +%!assert (gpinv (x, -1, ones (1,5), 0), y3) +%!assert (gpinv (x, -ones (1,5), 1, 0), y3) +%!assert (gpinv (x, -1, 1, 0), y3) +%!assert (gpinv (x, -1, 1, [0, 0, NaN, 0, 0]), [y3(1:2), NaN, y3(4:5)]) +%!assert (gpinv (x, -1, [1, 1, NaN, 1, 1], 0), [y3(1:2), NaN, y3(4:5)]) +%!assert (gpinv (x, -[1, 1, NaN, 1, 1], 1, 0), [y3(1:2), NaN, y3(4:5)]) +%!assert (gpinv ([x(1:2), NaN, x(4:5)], -1, 1, 0), [y3(1:2), NaN, y3(4:5)]) ## Test class of input preserved %!assert (gpinv (single ([x, NaN]), 0, 1, 0), single ([y1, NaN])) -%!assert (gpinv ([x, NaN], single (0), 1, 0), single ([y1, NaN])) -%!assert (gpinv ([x, NaN], 0, single (1), 0), single ([y1, NaN])) %!assert (gpinv ([x, NaN], 0, 1, single (0)), single ([y1, NaN])) +%!assert (gpinv ([x, NaN], 0, single (1), 0), single ([y1, NaN])) +%!assert (gpinv ([x, NaN], single (0), 1, 0), single ([y1, NaN])) -%!assert (gpinv (single ([x, NaN]), 0, 1, 1), single ([y2, NaN])) -%!assert (gpinv ([x, NaN], single (0), 1, 1), single ([y2, NaN])) -%!assert (gpinv ([x, NaN], 0, single (1), 1), single ([y2, NaN])) -%!assert (gpinv ([x, NaN], 0, 1, single (1)), single ([y2, NaN])) - -%!assert (gpinv (single ([x, NaN]), 0, 1, -1), single ([y3, NaN])) -%!assert (gpinv ([x, NaN], single (0), 1, -1), single ([y3, NaN])) -%!assert (gpinv ([x, NaN], 0, single (1), -1), single ([y3, NaN])) -%!assert (gpinv ([x, NaN], 0, 1, single (-1)), single ([y3, NaN])) +%!assert (gpinv (single ([x, NaN]), 1, 1, 0), single ([y2, NaN])) +%!assert (gpinv ([x, NaN], 1, 1, single (0)), single ([y2, NaN])) +%!assert (gpinv ([x, NaN], 1, single (1), 0), single ([y2, NaN])) +%!assert (gpinv ([x, NaN], single (1), 1, 0), single ([y2, NaN])) + +%!assert (gpinv (single ([x, NaN]), -1, 1, 0), single ([y3, NaN])) +%!assert (gpinv ([x, NaN], -1, 1, single (0)), single ([y3, NaN])) +%!assert (gpinv ([x, NaN], -1, single (1), 0), single ([y3, NaN])) +%!assert (gpinv ([x, NaN], single (-1), 1, 0), single ([y3, NaN])) ## Test input validation %!error gpinv () diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/gppdf.m new/statistics-1.4.1/inst/gppdf.m --- old/statistics-1.4.0/inst/gppdf.m 2018-05-19 06:40:09.374499307 +0200 +++ new/statistics-1.4.1/inst/gppdf.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,3 +1,4 @@ +## Copyright (C) 2018 John Donoghue ## Copyright (C) 2016 Dag Lyberg ## Copyright (C) 1997-2015 Kurt Hornik ## @@ -18,7 +19,7 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} gppdf (@var{x}, @var{location}, @var{scale}, @var{shape}) +## @deftypefn {} {} gppdf (@var{x}, @var{shape}, @var{scale}, @var{location}) ## Compute the probability density function (PDF) at @var{x} of the ## generalized Pareto distribution with parameters @var{location}, @var{scale}, ## and @var{shape}. @@ -27,7 +28,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: PDF of the generalized Pareto distribution -function pdf = gppdf (x, location, scale, shape) +function pdf = gppdf (x, shape, scale, location) if (nargin != 4) print_usage (); @@ -69,13 +70,13 @@ j = k & (shape > 0) & (z >= 0); if (any (j)) - pdf(j) = (shape * z(j) + 1).^(-(shape + 1) / shape); + pdf(j) = (shape * z(j) + 1).^(-(shape + 1) / shape) ./ scale; endif if (shape < 0) j = k & (shape < 0) & (0 <= z) & (z <= -1. / shape); if (any (j)) - pdf(j) = (shape * z(j) + 1).^(-(shape + 1) / shape); + pdf(j) = (shape * z(j) + 1).^(-(shape + 1) / shape) ./ scale; endif endif else @@ -88,13 +89,13 @@ j = k & (shape > 0) & (z >= 0); if (any (j)) - pdf(j) = (shape(j) .* z(j) + 1).^(-(shape(j) + 1) ./ shape(j)); + pdf(j) = (shape(j) .* z(j) + 1).^(-(shape(j) + 1) ./ shape(j)) ./ scale(j); endif if (any (shape < 0)) j = k & (shape < 0) & (0 <= z) & (z <= -1 ./ shape); if (any (j)) - pdf(j) = (shape(j) .* z(j) + 1).^(-(shape(j) + 1) ./ shape(j)); + pdf(j) = (shape(j) .* z(j) + 1).^(-(shape(j) + 1) ./ shape(j)) ./ scale(j); endif endif endif @@ -108,50 +109,50 @@ %! y2 = [0, 0, 1, 4/9, 1/4, 0]; %! y3 = [0, 0, 1, 1, 1, 0]; %!assert (gppdf (x, zeros (1,6), ones (1,6), zeros (1,6)), y1, eps) -%!assert (gppdf (x, zeros (1,6), 1, 0), y1, eps) -%!assert (gppdf (x, 0, ones (1,6), 0), y1, eps) %!assert (gppdf (x, 0, 1, zeros (1,6)), y1, eps) +%!assert (gppdf (x, 0, ones (1,6), 0), y1, eps) +%!assert (gppdf (x, zeros (1,6), 1, 0), y1, eps) %!assert (gppdf (x, 0, 1, 0), y1, eps) -%!assert (gppdf (x, [0, 0, 0, NaN, 0, 0], 1, 0), [y1(1:3), NaN, y1(5:6)]) -%!assert (gppdf (x, 0, [1, 1, 1, NaN, 1, 1], 0), [y1(1:3), NaN, y1(5:6)]) %!assert (gppdf (x, 0, 1, [0, 0, 0, NaN, 0, 0]), [y1(1:3), NaN, y1(5:6)]) +%!assert (gppdf (x, 0, [1, 1, 1, NaN, 1, 1], 0), [y1(1:3), NaN, y1(5:6)]) +%!assert (gppdf (x, [0, 0, 0, NaN, 0, 0], 1, 0), [y1(1:3), NaN, y1(5:6)]) %!assert (gppdf ([x(1:3), NaN, x(5:6)], 0, 1, 0), [y1(1:3), NaN, y1(5:6)]) -%!assert (gppdf (x, zeros (1,6), ones (1,6), ones (1,6)), y2, eps) -%!assert (gppdf (x, zeros (1,6), 1, 1), y2, eps) -%!assert (gppdf (x, 0, ones (1,6), 1), y2, eps) -%!assert (gppdf (x, 0, 1, ones (1,6)), y2, eps) -%!assert (gppdf (x, 0, 1, 1), y2, eps) -%!assert (gppdf (x, [0, 0, 0, NaN, 0, 0], 1, 1), [y2(1:3), NaN, y2(5:6)]) -%!assert (gppdf (x, 0, [1, 1, 1, NaN, 1, 1], 1), [y2(1:3), NaN, y2(5:6)]) -%!assert (gppdf (x, 0, 1, [1, 1, 1, NaN, 1, 1]), [y2(1:3), NaN, y2(5:6)]) -%!assert (gppdf ([x(1:3), NaN, x(5:6)], 0, 1, 1), [y2(1:3), NaN, y2(5:6)]) - -%!assert (gppdf (x, zeros (1,6), ones (1,6), -ones (1,6)), y3, eps) -%!assert (gppdf (x, zeros (1,6), 1, -1), y3, eps) -%!assert (gppdf (x, 0, ones (1,6), -1), y3, eps) -%!assert (gppdf (x, 0, 1, -ones (1,6)), y3, eps) -%!assert (gppdf (x, 0, 1, -1), y3, eps) -%!assert (gppdf (x, [0, 0, 0, NaN, 0, 0], 1, -1), [y3(1:3), NaN, y3(5:6)]) -%!assert (gppdf (x, 0, [1, 1, 1, NaN, 1, 1], -1), [y3(1:3), NaN, y3(5:6)]) -%!assert (gppdf (x, 0, 1, [-1, -1, -1, NaN, -1, -1]), [y3(1:3), NaN, y3(5:6)]) -%!assert (gppdf ([x(1:3), NaN, x(5:6)], 0, 1, -1), [y3(1:3), NaN, y3(5:6)]) +%!assert (gppdf (x, ones (1,6), ones (1,6), zeros (1,6)), y2, eps) +%!assert (gppdf (x, 1, 1, zeros (1,6)), y2, eps) +%!assert (gppdf (x, 1, ones (1,6), 0), y2, eps) +%!assert (gppdf (x, ones (1,6), 1, 0), y2, eps) +%!assert (gppdf (x, 1, 1, 0), y2, eps) +%!assert (gppdf (x, 1, 1, [0, 0, 0, NaN, 0, 0]), [y2(1:3), NaN, y2(5:6)]) +%!assert (gppdf (x, 1, [1, 1, 1, NaN, 1, 1], 0), [y2(1:3), NaN, y2(5:6)]) +%!assert (gppdf (x, [1, 1, 1, NaN, 1, 1], 1, 0), [y2(1:3), NaN, y2(5:6)]) +%!assert (gppdf ([x(1:3), NaN, x(5:6)], 1, 1, 0), [y2(1:3), NaN, y2(5:6)]) + +%!assert (gppdf (x, -ones (1,6), ones (1,6), zeros (1,6)), y3, eps) +%!assert (gppdf (x, -1, 1, zeros (1,6)), y3, eps) +%!assert (gppdf (x, -1, ones (1,6), 0), y3, eps) +%!assert (gppdf (x, -ones (1,6), 1, 0), y3, eps) +%!assert (gppdf (x, -1, 1, 0), y3, eps) +%!assert (gppdf (x, -1, 1, [0, 0, 0, NaN, 0, 0]), [y3(1:3), NaN, y3(5:6)]) +%!assert (gppdf (x, -1, [1, 1, 1, NaN, 1, 1], 0), [y3(1:3), NaN, y3(5:6)]) +%!assert (gppdf (x, [-1, -1, -1, NaN, -1, -1], 1, 0), [y3(1:3), NaN, y3(5:6)]) +%!assert (gppdf ([x(1:3), NaN, x(5:6)], -1, 1, 0), [y3(1:3), NaN, y3(5:6)]) ## Test class of input preserved %!assert (gppdf (single ([x, NaN]), 0, 1, 0), single ([y1, NaN])) -%!assert (gppdf ([x, NaN], single (0), 1, 0), single ([y1, NaN])) -%!assert (gppdf ([x, NaN], 0, single (1), 0), single ([y1, NaN])) %!assert (gppdf ([x, NaN], 0, 1, single (0)), single ([y1, NaN])) +%!assert (gppdf ([x, NaN], 0, single (1), 0), single ([y1, NaN])) +%!assert (gppdf ([x, NaN], single (0), 1, 0), single ([y1, NaN])) -%!assert (gppdf (single ([x, NaN]), 0, 1, 1), single ([y2, NaN])) -%!assert (gppdf ([x, NaN], single (0), 1, 1), single ([y2, NaN])) -%!assert (gppdf ([x, NaN], 0, single (1), 1), single ([y2, NaN])) -%!assert (gppdf ([x, NaN], 0, 1, single (1)), single ([y2, NaN])) - -%!assert (gppdf (single ([x, NaN]), 0, 1, -1), single ([y3, NaN])) -%!assert (gppdf ([x, NaN], single (0), 1, -1), single ([y3, NaN])) -%!assert (gppdf ([x, NaN], 0, single (1), -1), single ([y3, NaN])) -%!assert (gppdf ([x, NaN], 0, 1, single (-1)), single ([y3, NaN])) +%!assert (gppdf (single ([x, NaN]), 1, 1, 0), single ([y2, NaN])) +%!assert (gppdf ([x, NaN], 1, 1, single (0)), single ([y2, NaN])) +%!assert (gppdf ([x, NaN], 1, single (1), 0), single ([y2, NaN])) +%!assert (gppdf ([x, NaN], single (1), 1, 0), single ([y2, NaN])) + +%!assert (gppdf (single ([x, NaN]), -1, 1, 0), single ([y3, NaN])) +%!assert (gppdf ([x, NaN], -1, 1, single (0)), single ([y3, NaN])) +%!assert (gppdf ([x, NaN], -1, single (1), 0), single ([y3, NaN])) +%!assert (gppdf ([x, NaN], single (-1), 1, 0), single ([y3, NaN])) ## Test input validation %!error gppdf () @@ -159,9 +160,9 @@ %!error gppdf (1,2) %!error gppdf (1,2,3) %!error gppdf (1,2,3,4,5) -%!error gppdf (1, ones (3), ones (2), ones (2)) -%!error gppdf (1, ones (2), ones (3), ones (2)) %!error gppdf (1, ones (2), ones (2), ones (3)) +%!error gppdf (1, ones (2), ones (3), ones (2)) +%!error gppdf (1, ones (3), ones (2), ones (2)) %!error gppdf (i, 2, 2, 2) %!error gppdf (2, i, 2, 2) %!error gppdf (2, 2, i, 2) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/gprnd.m new/statistics-1.4.1/inst/gprnd.m --- old/statistics-1.4.0/inst/gprnd.m 2018-05-19 06:40:09.374499307 +0200 +++ new/statistics-1.4.1/inst/gprnd.m 2019-03-17 14:45:17.000000000 +0100 @@ -18,10 +18,10 @@ ## <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {} {} gprnd (@var{location}, @var{scale}, @var{shape}) -## @deftypefnx {} {} gprnd (@var{location}, @var{scale}, @var{shape}, @var{r}) -## @deftypefnx {} {} gprnd (@var{location}, @var{scale}, @var{shape}, @var{r}, @var{c}, @dots{}) -## @deftypefnx {} {} gprnd (@var{location}, @var{scale}, @var{shape}, [@var{sz}]) +## @deftypefn {} {} gprnd (@var{shape}, @var{scale}, @var{location}) +## @deftypefnx {} {} gprnd (@var{shape}, @var{scale}, @var{location}, @var{r}) +## @deftypefnx {} {} gprnd (@var{shape}, @var{scale}, @var{location}, @var{r}, @var{c}, @dots{}) +## @deftypefnx {} {} gprnd (@var{shape}, @var{scale}, @var{location}, [@var{sz}]) ## Return a matrix of random samples from the generalized Pareto distribution ## with parameters @var{location}, @var{scale} and @var{shape}. ## @@ -38,7 +38,7 @@ ## Author: Dag Lyberg <daglyberg80@gmail.com> ## Description: Random deviates from the generalized Pareto distribution -function rnd = gprnd (location, scale, shape, varargin) +function rnd = gprnd (shape, scale, location, varargin) if (nargin < 3) print_usage (); @@ -114,61 +114,61 @@ %!assert (size (gprnd (0,1,0)), [1, 1]) -%!assert (size (gprnd (zeros (2,1), 1,0)), [2, 1]) -%!assert (size (gprnd (zeros (2,2), 1,0)), [2, 2]) +%!assert (size (gprnd (0, 1, zeros (2,1))), [2, 1]) +%!assert (size (gprnd (0, 1, zeros (2,2))), [2, 2]) %!assert (size (gprnd (0, ones (2,1), 0)), [2, 1]) %!assert (size (gprnd (0, ones (2,2), 0)), [2, 2]) -%!assert (size (gprnd (0,1, zeros (2,1))), [2, 1]) -%!assert (size (gprnd (0,1, zeros (2,2))), [2, 2]) -%!assert (size (gprnd (0,1, 0, 3)), [3, 3]) -%!assert (size (gprnd (0,1, 0, [4 1])), [4, 1]) -%!assert (size (gprnd (0,1, 0, 4, 1)), [4, 1]) - -%!assert (size (gprnd (0,1,1)), [1, 1]) -%!assert (size (gprnd (zeros (2,1), 1,1)), [2, 1]) -%!assert (size (gprnd (zeros (2,2), 1,1)), [2, 2]) -%!assert (size (gprnd (0, ones (2,1), 1)), [2, 1]) -%!assert (size (gprnd (0, ones (2,2), 1)), [2, 2]) -%!assert (size (gprnd (0,1, ones (2,1))), [2, 1]) -%!assert (size (gprnd (0,1, ones (2,2))), [2, 2]) -%!assert (size (gprnd (0,1, 1, 3)), [3, 3]) -%!assert (size (gprnd (0,1, 1, [4 1])), [4, 1]) -%!assert (size (gprnd (0,1, 1, 4, 1)), [4, 1]) - -%!assert (size (gprnd (0,1,-1)), [1, 1]) -%!assert (size (gprnd (zeros (2,1), -1,1)), [2, 1]) -%!assert (size (gprnd (zeros (2,2), -1,1)), [2, 2]) -%!assert (size (gprnd (0, ones (2,1), -1)), [2, 1]) -%!assert (size (gprnd (0, ones (2,2), -1)), [2, 2]) -%!assert (size (gprnd (0,1, -ones (2,1))), [2, 1]) -%!assert (size (gprnd (0,1, -ones (2,2))), [2, 2]) -%!assert (size (gprnd (0,1, -1, 3)), [3, 3]) -%!assert (size (gprnd (0,1, -1, [4 1])), [4, 1]) -%!assert (size (gprnd (0,1, -1, 4, 1)), [4, 1]) +%!assert (size (gprnd (zeros (2,1), 1, 0)), [2, 1]) +%!assert (size (gprnd (zeros (2,2), 1, 0)), [2, 2]) +%!assert (size (gprnd (0, 1, 0, 3)), [3, 3]) +%!assert (size (gprnd (0, 1, 0, [4 1])), [4, 1]) +%!assert (size (gprnd (0, 1, 0, 4, 1)), [4, 1]) + +%!assert (size (gprnd (1,1,0)), [1, 1]) +%!assert (size (gprnd (1, 1, zeros (2,1))), [2, 1]) +%!assert (size (gprnd (1, 1, zeros (2,2))), [2, 2]) +%!assert (size (gprnd (1, ones (2,1), 0)), [2, 1]) +%!assert (size (gprnd (1, ones (2,2), 0)), [2, 2]) +%!assert (size (gprnd (ones (2,1), 1, 0)), [2, 1]) +%!assert (size (gprnd (ones (2,2), 1, 0)), [2, 2]) +%!assert (size (gprnd (1, 1, 0, 3)), [3, 3]) +%!assert (size (gprnd (1, 1, 0, [4 1])), [4, 1]) +%!assert (size (gprnd (1, 1, 0, 4, 1)), [4, 1]) + +%!assert (size (gprnd (-1, 1, 0)), [1, 1]) +%!assert (size (gprnd (-1, 1, zeros (2,1))), [2, 1]) +%!assert (size (gprnd (1, -1, zeros (2,2))), [2, 2]) +%!assert (size (gprnd (-1, ones (2,1), 0)), [2, 1]) +%!assert (size (gprnd (-1, ones (2,2), 0)), [2, 2]) +%!assert (size (gprnd (-ones (2,1), 1, 0)), [2, 1]) +%!assert (size (gprnd (-ones (2,2), 1, 0)), [2, 2]) +%!assert (size (gprnd (-1, 1, 0, 3)), [3, 3]) +%!assert (size (gprnd (-1, 1, 0, [4 1])), [4, 1]) +%!assert (size (gprnd (-1, 1, 0, 4, 1)), [4, 1]) ## Test class of input preserved %!assert (class (gprnd (0,1,0)), "double") -%!assert (class (gprnd (single (0),1,0)), "single") -%!assert (class (gprnd (single ([0 0]),1,0)), "single") +%!assert (class (gprnd (0, 1, single (0))), "single") +%!assert (class (gprnd (0, 1, single ([0 0]))), "single") %!assert (class (gprnd (0,single (1),0)), "single") %!assert (class (gprnd (0,single ([1 1]),0)), "single") -%!assert (class (gprnd (0,1,single (0))), "single") -%!assert (class (gprnd (0,1,single ([0 0]))), "single") +%!assert (class (gprnd (single (0), 1, 0)), "single") +%!assert (class (gprnd (single ([0 0]), 1, 0)), "single") ## Test input validation %!error gprnd () %!error gprnd (1) %!error gprnd (1,2) -%!error gprnd (zeros (3), ones (2), zeros (2)) -%!error gprnd (zeros (2), ones (3), zeros (2)) %!error gprnd (zeros (2), ones (2), zeros (3)) +%!error gprnd (zeros (2), ones (3), zeros (2)) +%!error gprnd (zeros (3), ones (2), zeros (2)) %!error gprnd (i, 1, 0) %!error gprnd (0, i, 0) %!error gprnd (0, 1, i) %!error gprnd (0,1,0, -1) %!error gprnd (0,1,0, ones (2)) %!error gprnd (0,1,0, [2 -1 2]) -%!error gprnd (zeros (2),1,0, 3) -%!error gprnd (zeros (2),1,0, [3, 2]) -%!error gprnd (zeros (2),1,0, 3, 2) +%!error gprnd (0,1, zeros (2), 3) +%!error gprnd (0,1, zeros (2), [3, 2]) +%!error gprnd (0,1, zeros (2), 3, 2) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/monotone_smooth.m new/statistics-1.4.1/inst/monotone_smooth.m --- old/statistics-1.4.0/inst/monotone_smooth.m 2018-05-19 06:40:09.382499268 +0200 +++ new/statistics-1.4.1/inst/monotone_smooth.m 2019-03-17 14:45:17.000000000 +0100 @@ -17,7 +17,9 @@ ## -*- texinfo -*- ## @deftypefn {Function File} {@var{yy} =} monotone_smooth (@var{x}, @var{y}, @var{h}) ## Produce a smooth monotone increasing approximation to a sampled functional -## dependence y(x) using a kernel method (an Epanechnikov smoothing kernel is +## dependence +## +## A kernel method is used (an Epanechnikov smoothing kernel is ## applied to y(x); this is integrated to yield the monotone increasing form. ## See Reference 1 for details.) ## diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/pcacov.m new/statistics-1.4.1/inst/pcacov.m --- old/statistics-1.4.0/inst/pcacov.m 2018-05-19 06:40:09.390499229 +0200 +++ new/statistics-1.4.1/inst/pcacov.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,4 @@ -## Copyright (C) 2013 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> +## Copyright (C) 2013-2019 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> ## ## This program is free software; you can redistribute it and/or ## modify it under the terms of the GNU General Public License @@ -16,10 +16,10 @@ ## @deftypefn {Function File} {[@var{COEFF}]} = pcacov(@var{X}) ## @deftypefnx {Function File} {[@var{COEFF},@var{latent}]} = pcacov(@var{X}) ## @deftypefnx {Function File} {[@var{COEFF},@var{latent},@var{explained}]} = pcacov(@var{X}) +## Perform principal component analysis on the nxn covariance matrix X +## ## @itemize @bullet ## @item -## pcacov performs principal component analysis on the nxn covariance matrix X -## @item ## @var{COEFF} : a nxn matrix with columns containing the principal component coefficients ## @item ## @var{latent} : a vector containing the principal component variances diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/pcares.m new/statistics-1.4.1/inst/pcares.m --- old/statistics-1.4.0/inst/pcares.m 2018-05-19 06:40:09.390499229 +0200 +++ new/statistics-1.4.1/inst/pcares.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,4 @@ -## Copyright (C) 2013 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> +## Copyright (C) 2013-2019 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> ## ## This program is free software; you can redistribute it and/or ## modify it under the terms of the GNU General Public License @@ -14,6 +14,8 @@ ## -*- texinfo -*- ## @deftypefn {Function File} {[@var{residuals},@var{reconstructed}]}=pcares(@var{X}, @var{NDIM}) +## Calulate residuals from principal component analysis +## ## @itemize @bullet ## @item ## @var{X} : N x P Matrix with N observations and P variables, the variables will be mean centered diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/pdist2.m new/statistics-1.4.1/inst/pdist2.m --- old/statistics-1.4.0/inst/pdist2.m 2018-05-19 06:40:09.390499229 +0200 +++ new/statistics-1.4.1/inst/pdist2.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,4 @@ -## Copyright (C) 2014 Piotr Dollar <pdollar@gmail.com> +## Copyright (C) 2014-2019 Piotr Dollar <pdollar@gmail.com> ## ## This program is free software; you can redistribute it and/or ## modify it under the terms of the GNU General Public License as @@ -152,7 +152,7 @@ function dists = distEucSq (x, y) xx = sumsq (x, 2); yy = sumsq (y, 2)'; - dists = bsxfun (@plus, xx, yy) - 2 * x * (y'); + dists = max (0, bsxfun (@plus, xx, yy) - 2 * x * (y')); endfunction ## euclidean distance as loop for testing purposes diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/plsregress.m new/statistics-1.4.1/inst/plsregress.m --- old/statistics-1.4.0/inst/plsregress.m 2018-05-19 06:40:09.390499229 +0200 +++ new/statistics-1.4.1/inst/plsregress.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,4 @@ -## Copyright (C) 2012 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> +## Copyright (C) 2012-2019 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> ## ## This program is free software; you can redistribute it and/or ## modify it under the terms of the GNU General Public License @@ -13,8 +13,9 @@ ## this program; if not, see <http://www.gnu.org/licenses/>. ## -*- texinfo -*- -## @deftypefn {Function File} {[@var{XLOADINGS},@var{YLOADINGS},@var{XSCORES},@var{YSCORES},@var{coefficients},@var{fitted}] =} ... -## plsregress(@var{X}, @var{Y}, @var{NCOMP}) +## @deftypefn {Function File} {[@var{XLOADINGS},@var{YLOADINGS},@var{XSCORES},@var{YSCORES},@var{coefficients},@var{fitted}] =} plsregress(@var{X}, @var{Y}, @var{NCOMP}) +## Calculate partial least squares regression +## ## @itemize @bullet ## @item ## @var{X}: Matrix of observations diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/princomp.m new/statistics-1.4.1/inst/princomp.m --- old/statistics-1.4.0/inst/princomp.m 2018-05-19 06:40:09.390499229 +0200 +++ new/statistics-1.4.1/inst/princomp.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,4 @@ -## Copyright (C) 2013 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> +## Copyright (C) 2013-2019 Fernando Damian Nieuwveldt <fdnieuwveldt@gmail.com> ## ## This program is free software; you can redistribute it and/or ## modify it under the terms of the GNU General Public License @@ -18,10 +18,10 @@ ## @deftypefnx {Function File} {[@var{COEFF},@var{SCORE},@var{latent}]} = princomp(@var{X}) ## @deftypefnx {Function File} {[@var{COEFF},@var{SCORE},@var{latent},@var{tsquare}]} = princomp(@var{X}) ## @deftypefnx {Function File} {[...]} = princomp(@var{X},'econ') +## Performs a principal component analysis on a NxP data matrix X +## ## @itemize @bullet ## @item -## princomp performs principal component analysis on a NxP data matrix X -## @item ## @var{COEFF} : returns the principal component coefficients ## @item ## @var{SCORE} : returns the principal component scores, the representation of X diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/ttest.m new/statistics-1.4.1/inst/ttest.m --- old/statistics-1.4.0/inst/ttest.m 2018-05-19 06:40:09.402499170 +0200 +++ new/statistics-1.4.1/inst/ttest.m 2019-03-17 14:45:17.000000000 +0100 @@ -154,7 +154,7 @@ %! [h, pval, ci0] = ttest (x, 0); %! assert (h, 1) %! assert (pval, 0) -%! assert (ci0, ci) +%! assert (ci0, ci, 2e-15) %! [h, pval, ci] = ttest (x, 10, "tail", "right", "dim", 2, "alpha", 0.05); %! assert (h, 0) %! assert (pval, 0.5, 10*eps) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/inst/wishrnd.m new/statistics-1.4.1/inst/wishrnd.m --- old/statistics-1.4.0/inst/wishrnd.m 2018-05-19 06:40:09.406499150 +0200 +++ new/statistics-1.4.1/inst/wishrnd.m 2019-03-17 14:45:17.000000000 +0100 @@ -1,4 +1,4 @@ -## Copyright (C) 2013 Nir Krakauer <nkrakauer@ccny.cuny.edu> +## Copyright (C) 2013-2019 Nir Krakauer <mail@nirkrakauer.net> ## ## 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. ## @@ -10,10 +10,10 @@ ## @deftypefn {Function File} {} [@var{W}[, @var{D}]] = wishrnd (@var{Sigma}, @var{df}[, @var{D}][, @var{n}=1]) ## Return a random matrix sampled from the Wishart distribution with given parameters ## -## Inputs: the @var{p} x @var{p} positive definite matrix @var{Sigma} and scalar degrees of freedom parameter @var{df} (and optionally the Cholesky factor @var{D} of @var{Sigma}). +## Inputs: the @var{p} x @var{p} positive definite matrix @var{Sigma} (or the lower-triangular Cholesky factor @var{D} of @var{Sigma}) and scalar degrees of freedom parameter @var{df}. ## @var{df} can be non-integer as long as @var{df} > @var{p} ## -## Output: a random @var{p} x @var{p} matrix @var{W} from the Wishart(@var{Sigma}, @var{df}) distribution. If @var{n} > 1, then @var{W} is @var{p} x @var{p} x @var{n} and holds @var{n} such random matrices. (Optionally, the Cholesky factor @var{D} of @var{Sigma} is also returned.) +## Output: a random @var{p} x @var{p} matrix @var{W} from the Wishart(@var{Sigma}, @var{df}) distribution. If @var{n} > 1, then @var{W} is @var{p} x @var{p} x @var{n} and holds @var{n} such random matrices. (Optionally, the lower-triangular Cholesky factor @var{D} of @var{Sigma} is also returned.) ## ## Averaged across many samples, the mean of @var{W} should approach @var{df}*@var{Sigma}, and the variance of each element @var{W}_ij should approach @var{df}*(@var{Sigma}_ij^2 + @var{Sigma}_ii*@var{Sigma}_jj) ## @@ -22,8 +22,8 @@ ## @seealso{iwishrnd, wishpdf} ## @end deftypefn -## Author: Nir Krakauer <nkrakauer@ccny.cuny.edu> -## Description: Compute the probability density function of the Wishart distribution +## Author: Nir Krakauer <mail@nirkrakauer.net> +## Description: Sample from the Wishart distribution function [W, D] = wishrnd(Sigma, df, D, n=1) @@ -33,7 +33,7 @@ if nargin < 3 || isempty(D) try - D = chol(Sigma); + D = chol(Sigma, 'lower'); catch error('wishrnd: Cholesky decomposition failed; Sigma probably not positive definite') end_try_catch @@ -59,23 +59,21 @@ for i = 1:n if df_isint - Z = randn(df, p) * D; - W(:, :, i) = Z'*Z; + Z = D * randn(p, df); else Z = diag(sqrt(chi2rnd(df - (0:(p-1))))); #fill diagonal #note: chi2rnd(x) is equivalent to 2*randg(x/2), but the latter seems to offer no performance advantage Z(ii > jj) = randn(p*(p-1)/2, 1); #fill lower triangle with normally distributed variates Z = D * Z; - W(:, :, i) = Z*Z'; endif - - + W(:, :, i) = Z*Z'; endfor endfunction - +%!assert(size (wishrnd (1,2)), [1, 1]); +%!assert(size (wishrnd (1,2,[])), [1, 1]); %!assert(size (wishrnd (1,2,1)), [1, 1]); %!assert(size (wishrnd ([],2,1)), [1, 1]); %!assert(size (wishrnd ([3 1; 1 3], 2.00001, [], 1)), [2, 2]); diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/install-conditionally/distributions/normpdf.m new/statistics-1.4.1/install-conditionally/distributions/normpdf.m --- old/statistics-1.4.0/install-conditionally/distributions/normpdf.m 2018-05-19 06:40:09.434499012 +0200 +++ new/statistics-1.4.1/install-conditionally/distributions/normpdf.m 2019-03-17 14:45:17.000000000 +0100 @@ -71,12 +71,12 @@ %!shared x,y %! x = [-Inf 1 2 Inf]; %! y = 1/sqrt(2*pi)*exp (-(x-1).^2/2); -%!assert (normpdf (x, ones (1,4), ones (1,4)), y) -%!assert (normpdf (x, 1, ones (1,4)), y) -%!assert (normpdf (x, ones (1,4), 1), y) -%!assert (normpdf (x, [0 -Inf NaN Inf], 1), [y(1) NaN NaN NaN]) -%!assert (normpdf (x, 1, [Inf NaN -1 0]), [NaN NaN NaN NaN]) -%!assert (normpdf ([x, NaN], 1, 1), [y, NaN]) +%!assert (normpdf (x, ones (1,4), ones (1,4)), y, eps) +%!assert (normpdf (x, 1, ones (1,4)), y, eps) +%!assert (normpdf (x, ones (1,4), 1), y, eps) +%!assert (normpdf (x, [0 -Inf NaN Inf], 1), [y(1) NaN NaN NaN], eps) +%!assert (normpdf (x, 1, [Inf NaN -1 0]), [NaN NaN NaN NaN], eps) +%!assert (normpdf ([x, NaN], 1, 1), [y, NaN], eps) ## Test class of input preserved %!assert (normpdf (single ([x, NaN]), 1, 1), single ([y, NaN]), eps ("single")) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/install-conditionally/tests/bartlett_test.m new/statistics-1.4.1/install-conditionally/tests/bartlett_test.m --- old/statistics-1.4.0/install-conditionally/tests/bartlett_test.m 2018-05-19 06:40:09.446498953 +0200 +++ new/statistics-1.4.1/install-conditionally/tests/bartlett_test.m 2019-03-17 14:45:17.000000000 +0100 @@ -55,7 +55,7 @@ v_tot = sum (f .* v) / f_tot; c = 1 + (sum (1 ./ f) - 1 / f_tot) / (3 * (k - 1)); chisq = (f_tot * log (v_tot) - sum (f .* log (v))) / c; - df = k; + df = k - 1; pval = 1 - chi2cdf (chisq, df); if (nargout == 0) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/install-conditionally/tests/t_test.m new/statistics-1.4.1/install-conditionally/tests/t_test.m --- old/statistics-1.4.0/install-conditionally/tests/t_test.m 2018-05-19 06:40:09.450498934 +0200 +++ new/statistics-1.4.1/install-conditionally/tests/t_test.m 2019-03-17 14:45:17.000000000 +0100 @@ -93,7 +93,7 @@ %! tval = -abs (tinv (0.5*pval, n-1)); %! endif %! unew = tval * std(x)/sqrt(n) + u0; -%! assert (xbar, unew, 1000*eps); +%! assert (xbar, unew, 1e6*eps); %!test %! x = rand (10,1); n = length (x); @@ -101,7 +101,7 @@ %! pval = t_test (x, u0, ">"); %! tval = tinv (1-pval, n-1); %! unew = tval * std(x)/sqrt(n) + u0; -%! assert (mean (x), unew, 1000*eps); +%! assert (mean (x), unew, 1e6*eps); %!test %! x = rand (10,1); n = length (x); @@ -109,4 +109,4 @@ %! pval = t_test (x, u0, "<"); %! tval = tinv (pval, n-1); %! unew = tval * std(x)/sqrt(n) + u0; -%! assert (mean (x), unew, 1000*eps); +%! assert (mean (x), unew, 1e6*eps); diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/src/configure.ac new/statistics-1.4.1/src/configure.ac --- old/statistics-1.4.0/src/configure.ac 2018-05-19 06:40:09.454498915 +0200 +++ new/statistics-1.4.1/src/configure.ac 2019-03-17 14:45:17.000000000 +0100 @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ([2.69]) -AC_INIT([statistics], [1.4.0]) +AC_INIT([statistics], [1.4.1]) AC_CANONICAL_TARGET diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/utils/conditional_installation.m new/statistics-1.4.1/utils/conditional_installation.m --- old/statistics-1.4.0/utils/conditional_installation.m 2018-05-19 06:40:09.454498915 +0200 +++ new/statistics-1.4.1/utils/conditional_installation.m 2019-03-17 14:45:17.000000000 +0100 @@ -35,6 +35,10 @@ ## "functions_to_install")); # defines variable ## # 'install_functions' + if exist ("isfolder") == 0 + isfolder = @(n) isdir(n); + endif + installed_functions = {}; subdirs = {"base", "distributions", "models", "tests"}; @@ -51,7 +55,7 @@ assert_dir (fullfile (destdir, subdir)); - if (isdir (private_dir = fullfile (srcdir, subdir, "private")) + if (isfolder (private_dir = fullfile (srcdir, subdir, "private")) && ! ([status, msg] = ... copyfile (private_dir, fullfile (destdir, subdir)))) @@ -131,7 +135,11 @@ function assert_dir (directory) - if (! isdir (directory)) + if exist ("isfolder") == 0 + isfolder = @(n) isdir(n); + endif + + if (! isfolder (directory)) if (! ([succ, msg] = mkdir (directory))) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' --exclude Makefile.in --exclude configure --exclude config.guess --exclude '*.pot' --exclude mkinstalldirs --exclude aclocal.m4 --exclude config.sub --exclude depcomp --exclude install-sh --exclude ltmain.sh old/statistics-1.4.0/utils/functions_to_install new/statistics-1.4.1/utils/functions_to_install --- old/statistics-1.4.0/utils/functions_to_install 2018-05-19 06:40:09.454498915 +0200 +++ new/statistics-1.4.1/utils/functions_to_install 2019-03-17 14:45:17.000000000 +0100 @@ -15,6 +15,7 @@ ## "base/corr.m", ... ## "base/corrcoef.m", ... ## "base/cov.m", ... +## "base/crosstab.m", ... ## "base/gls.m", ... ## "base/histc.m", ... ## "base/iqr.m", ... @@ -22,6 +23,7 @@ ## "base/kurtosis.m", ... ## "base/logit.m", ... ## "base/lscov.m", ... +## "base/mad.m", ... ## "base/mean.m", ... ## "base/meansq.m", ... ## "base/median.m", ... @@ -41,112 +43,125 @@ ## "base/spearman.m", ... ## "base/statistics.m", ... ## "base/std.m", ... -## "base/table.m", ... ## "base/var.m", ... ## "base/zscore.m", ... ## ... -## "distributions/center.m", ... -## "distributions/cloglog.m", ... -## "distributions/corr.m", ... -## "distributions/corrcoef.m", ... -## "distributions/cov.m", ... -## "distributions/gls.m", ... -## "distributions/histc.m", ... -## "distributions/iqr.m", ... -## "distributions/kendall.m", ... -## "distributions/kurtosis.m", ... -## "distributions/logit.m", ... -## "distributions/lscov.m", ... -## "distributions/mean.m", ... -## "distributions/meansq.m", ... -## "distributions/median.m", ... -## "distributions/mode.m", ... -## "distributions/moment.m", ... -## "distributions/ols.m", ... -## "distributions/ppplot.m", ... -## "distributions/prctile.m", ... -## "distributions/probit.m", ... -## "distributions/qqplot.m", ... -## "distributions/quantile.m", ... -## "distributions/range.m", ... -## "distributions/ranks.m", ... -## "distributions/run_count.m", ... -## "distributions/runlength.m", ... -## "distributions/skewness.m", ... -## "distributions/spearman.m", ... -## "distributions/statistics.m", ... -## "distributions/std.m", ... -## "distributions/table.m", ... -## "distributions/var.m", ... -## "distributions/zscore.m", ... +## "distributions/betacdf.m", ... +## "distributions/betainv.m", ... +## "distributions/betapdf.m", ... +## "distributions/betarnd.m", ... +## "distributions/binocdf.m", ... +## "distributions/binoinv.m", ... +## "distributions/binopdf.m", ... +## "distributions/binornd.m", ... +## "distributions/cauchy_cdf.m", ... +## "distributions/cauchy_inv.m", ... +## "distributions/cauchy_pdf.m", ... +## "distributions/cauchy_rnd.m", ... +## "distributions/chi2cdf.m", ... +## "distributions/chi2inv.m", ... +## "distributions/chi2pdf.m", ... +## "distributions/chi2rnd.m", ... +## "distributions/discrete_cdf.m", ... +## "distributions/discrete_inv.m", ... +## "distributions/discrete_pdf.m", ... +## "distributions/discrete_rnd.m", ... +## "distributions/empirical_cdf.m", ... +## "distributions/empirical_inv.m", ... +## "distributions/empirical_pdf.m", ... +## "distributions/empirical_rnd.m", ... +## "distributions/expcdf.m", ... +## "distributions/expinv.m", ... +## "distributions/exppdf.m", ... +## "distributions/exprnd.m", ... +## "distributions/fcdf.m", ... +## "distributions/finv.m", ... +## "distributions/fpdf.m", ... +## "distributions/frnd.m", ... +## "distributions/gamcdf.m", ... +## "distributions/gaminv.m", ... +## "distributions/gampdf.m", ... +## "distributions/gamrnd.m", ... +## "distributions/geocdf.m", ... +## "distributions/geoinv.m", ... +## "distributions/geopdf.m", ... +## "distributions/geornd.m", ... +## "distributions/hygecdf.m", ... +## "distributions/hygeinv.m", ... +## "distributions/hygepdf.m", ... +## "distributions/hygernd.m", ... +## "distributions/kolmogorov_smirnov_cdf.m", ... +## "distributions/laplace_cdf.m", ... +## "distributions/laplace_inv.m", ... +## "distributions/laplace_pdf.m", ... +## "distributions/laplace_rnd.m", ... +## "distributions/logistic_cdf.m", ... +## "distributions/logistic_inv.m", ... +## "distributions/logistic_pdf.m", ... +## "distributions/logistic_rnd.m", ... +## "distributions/logncdf.m", ... +## "distributions/logninv.m", ... +## "distributions/lognpdf.m", ... +## "distributions/lognrnd.m", ... +## "distributions/nbincdf.m", ... +## "distributions/nbininv.m", ... +## "distributions/nbinpdf.m", ... +## "distributions/nbinrnd.m", ... +## "distributions/normcdf.m", ... +## "distributions/norminv.m", ... +## "distributions/normpdf.m", ... +## "distributions/normrnd.m", ... +## "distributions/poisscdf.m", ... +## "distributions/poissinv.m", ... +## "distributions/poisspdf.m", ... +## "distributions/poissrnd.m", ... +## "distributions/stdnormal_cdf.m", ... +## "distributions/stdnormal_inv.m", ... +## "distributions/stdnormal_pdf.m", ... +## "distributions/stdnormal_rnd.m", ... +## "distributions/tcdf.m", ... +## "distributions/tinv.m", ... +## "distributions/tpdf.m", ... +## "distributions/trnd.m", ... +## "distributions/unidcdf.m", ... +## "distributions/unidinv.m", ... +## "distributions/unidpdf.m", ... +## "distributions/unidrnd.m", ... +## "distributions/unifcdf.m", ... +## "distributions/unifinv.m", ... +## "distributions/unifpdf.m", ... +## "distributions/unifrnd.m", ... +## "distributions/wblcdf.m", ... +## "distributions/wblinv.m", ... +## "distributions/wblpdf.m", ... +## "distributions/wblrnd.m", ... +## "distributions/wienrnd.m", ... ## ... -## "models/center.m", ... -## "models/cloglog.m", ... -## "models/corr.m", ... -## "models/corrcoef.m", ... -## "models/cov.m", ... -## "models/gls.m", ... -## "models/histc.m", ... -## "models/iqr.m", ... -## "models/kendall.m", ... -## "models/kurtosis.m", ... -## "models/logit.m", ... -## "models/lscov.m", ... -## "models/mean.m", ... -## "models/meansq.m", ... -## "models/median.m", ... -## "models/mode.m", ... -## "models/moment.m", ... -## "models/ols.m", ... -## "models/ppplot.m", ... -## "models/prctile.m", ... -## "models/probit.m", ... -## "models/qqplot.m", ... -## "models/quantile.m", ... -## "models/range.m", ... -## "models/ranks.m", ... -## "models/run_count.m", ... -## "models/runlength.m", ... -## "models/skewness.m", ... -## "models/spearman.m", ... -## "models/statistics.m", ... -## "models/std.m", ... -## "models/table.m", ... -## "models/var.m", ... -## "models/zscore.m", ... +## "models/logistic_regression.m", ... ## ... -## "tests/center.m", ... -## "tests/cloglog.m", ... -## "tests/corr.m", ... -## "tests/corrcoef.m", ... -## "tests/cov.m", ... -## "tests/gls.m", ... -## "tests/histc.m", ... -## "tests/iqr.m", ... -## "tests/kendall.m", ... -## "tests/kurtosis.m", ... -## "tests/logit.m", ... -## "tests/lscov.m", ... -## "tests/mean.m", ... -## "tests/meansq.m", ... -## "tests/median.m", ... -## "tests/mode.m", ... -## "tests/moment.m", ... -## "tests/ols.m", ... -## "tests/ppplot.m", ... -## "tests/prctile.m", ... -## "tests/probit.m", ... -## "tests/qqplot.m", ... -## "tests/quantile.m", ... -## "tests/range.m", ... -## "tests/ranks.m", ... -## "tests/run_count.m", ... -## "tests/runlength.m", ... -## "tests/skewness.m", ... -## "tests/spearman.m", ... -## "tests/statistics.m", ... -## "tests/std.m", ... -## "tests/table.m", ... -## "tests/var.m", ... -## "tests/zscore.m" ... +## "tests/anova.m", ... +## "tests/bartlett_test.m", ... +## "tests/chisquare_test_homogeneity.m", ... +## "tests/chisquare_test_independence.m", ... +## "tests/cor_test.m", ... +## "tests/f_test_regression.m", ... +## "tests/hotelling_test_2.m", ... +## "tests/hotelling_test.m", ... +## "tests/kolmogorov_smirnov_test_2.m", ... +## "tests/kolmogorov_smirnov_test.m", ... +## "tests/kruskal_wallis_test.m", ... +## "tests/manova.m", ... +## "tests/mcnemar_test.m", ... +## "tests/prop_test_2.m", ... +## "tests/run_test.m", ... +## "tests/sign_test.m", ... +## "tests/t_test_2.m", ... +## "tests/t_test.m", ... +## "tests/t_test_regression.m", ... +## "tests/u_test.m", ... +## "tests/var_test.m", ... +## "tests/welch_test.m", ... +## "tests/wilcoxon_test.m", ... +## "tests/z_test_2.m", ... +## "tests/z_test.m" ... };