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Package is "octave-forge-nan" Wed Mar 17 20:16:43 2021 rev:12 rq:879588 version:3.5.3 Changes: -------- --- /work/SRC/openSUSE:Factory/octave-forge-nan/octave-forge-nan.changes 2020-12-04 21:27:56.902078371 +0100 +++ /work/SRC/openSUSE:Factory/.octave-forge-nan.new.2401/octave-forge-nan.changes 2021-03-17 20:20:04.859327858 +0100 @@ -1,0 +2,8 @@ +Sat Mar 13 13:56:09 UTC 2021 - Atri Bhattacharya <badshah...@gmail.com> + +- Update to version 3.5.3 + * kappa: Youden index (YI), and SSE as return value + * roc: add maxYI as output value + * naninsttest: check ttest for NaN handling + +------------------------------------------------------------------- Old: ---- nan-3.5.2.tar.gz New: ---- nan-3.5.3.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ octave-forge-nan.spec ++++++ --- /var/tmp/diff_new_pack.EhoqwO/_old 2021-03-17 20:20:05.315328482 +0100 +++ /var/tmp/diff_new_pack.EhoqwO/_new 2021-03-17 20:20:05.319328487 +0100 @@ -1,7 +1,7 @@ # # spec file for package octave-forge-nan # -# Copyright (c) 2020 SUSE LLC +# Copyright (c) 2021 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -18,7 +18,7 @@ %define octpkg nan Name: octave-forge-%{octpkg} -Version: 3.5.2 +Version: 3.5.3 Release: 0 Summary: A statistics and machine learning toolbox License: GPL-3.0-or-later ++++++ nan-3.5.2.tar.gz -> nan-3.5.3.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/DESCRIPTION new/nan-3.5.3/DESCRIPTION --- old/nan-3.5.2/DESCRIPTION 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/DESCRIPTION 2021-02-15 07:41:05.000000000 +0100 @@ -1,6 +1,6 @@ Name: NaN -Version: 3.5.2 -Date: 2020-10-31 +Version: 3.5.3 +Date: 2021-02-15 Author: Alois Schl??gl <alois.schlo...@gmail.com> Maintainer: Alois Schl??gl Title: The NaN-toolbox diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/NEWS new/nan-3.5.3/NEWS --- old/nan-3.5.2/NEWS 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/NEWS 2021-02-15 07:41:05.000000000 +0100 @@ -1,3 +1,9 @@ +2021-02-15: Release of NaN-toolbox 3.5.3 + +* kappa: Youden index (YI), and SSE as return value +* roc: add maxYI as output value +* naninsttest: check ttest for NaN handling + 2020-10-31: Release of NaN-toolbox 3.5.2 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/doc/README.TXT new/nan-3.5.3/doc/README.TXT --- old/nan-3.5.2/doc/README.TXT 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/doc/README.TXT 2021-02-15 07:41:05.000000000 +0100 @@ -1,6 +1,6 @@ NaN-Tb: A statistics toolbox ------------------------------------------------------------ -Copyright (C) 2000-2005,2009,2010,2011,2014 Alois Schloegl <alois.schlo...@gmail.com> +Copyright (C) 2000-2021 Alois Schl??gl <alois.schlo...@gmail.com> FEATURES of the NaN-tb: @@ -18,7 +18,7 @@ - fixes known bugs - compatible with Matlab and Octave - easy to use - - The toolbox is tested with Octave 3.x and Matlab 7.x + - The toolbox is tested with Octave 4.4+ and Matlab 7.x Currently are implemented: @@ -121,7 +121,7 @@ KAPPA performance evaluation TRAIN_LDA_SPARSE utility function FSS feature subset selection and feature ranking - CAT2BIN converts categorial to binary data + CAT2BIN converts categorical to binary data SVMTRAIN_MEX libSVM-training algorithm ROW_COL_DELETION heuristic to select rows and columns to remove missing values @@ -279,8 +279,7 @@ Run NANINSTTEST again to check the stability of the compiled SUMSKIPNAN. - $Id$ - Copyright (C) 2000-2005,2009,2010,2011,2014 by Alois Schloegl <alois.schlo...@gmail.com> + Copyright (C) 2000-2021 by Alois Schl??gl <alois.schlo...@gmail.com> http://pub.ist.ac.at/~schloegl/matlab/NaN/ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/inst/cat2bin.m new/nan-3.5.3/inst/cat2bin.m --- old/nan-3.5.2/inst/cat2bin.m 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/inst/cat2bin.m 2021-02-15 07:41:05.000000000 +0100 @@ -1,12 +1,12 @@ function [B,BLab]=cat2bin(D, Label, MODE) -% CAT2BIN converts categorial into binary data +% CAT2BIN converts categorical into binary data % each category of each column in D is converted into a logical column % % B = cat2bin(C); % [B,BinLabel] = cat2bin(C,Label); % [B,BinLabel] = cat2bin(C,Label,MODE) % -% C categorial data +% C categorical data % B binary data % Label description of each column in C % BinLabel description of each column in B diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/inst/kappa.m new/nan-3.5.3/inst/kappa.m --- old/nan-3.5.2/inst/kappa.m 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/inst/kappa.m 2021-02-15 07:41:05.000000000 +0100 @@ -21,8 +21,8 @@ % MI Mutual information or transfer information (in [bits]) % X is a struct containing all the fields above % For two classes, a number of additional summary statistics including -% TPR, FPR, FDR, PPV, NPF, F1, dprime, Matthews Correlation coefficient (MCC) or -% Phi coefficient (PHI=MCC), Specificity and Sensitivity +% TPR, FPR, FDR, PPV, NPF, F1, dprime, Matthews Correlation coefficient (MCC) or +% Phi coefficient (PHI=MCC), Specificity and Sensitivity, Youden index (YI) % are provided. Note, the positive category must the larger label (in d and c), otherwise % the confusion matrix becomes transposed and the summary statistics are messed up. % @@ -37,7 +37,7 @@ % [5] http://ourworld.compuserve.com/homepages/jsuebersax/kappa.htm % [6] http://en.wikipedia.org/wiki/Receiver_operating_characteristic -% Copyright (c) 1997-2020 by Alois Schloegl <alois.schlo...@gmail.com> +% Copyright (c) 1997-2021 by Alois Schloegl <alois.schlo...@gmail.com> % This function is part of the NaN-toolbox % http://pub.ist.ac.at/~schloegl/matlab/NaN/ % @@ -158,11 +158,12 @@ X.ACC = p0; X.sACC = SA; X.MI = R; +X.SSE = sum(X.data(:))-trace(X.data); X.datatype = 'confusion'; if length(H)==2, % see http://en.wikipedia.org/wiki/Receiver_operating_characteristic - % Note that the confusion matrix used here is has positive values in + % Note that the confusion matrix used here uses more positive values in % the 2nd row and column, moreover the true values are indicated by % rows (transposed). Thus, in summary H(1,1) and H(2,2) are exchanged % as compared to the wikipedia article. @@ -183,6 +184,7 @@ X.Specificity = 1 - X.FPR; X.Precision = X.PPV; X.dprime = norminv(X.TPR) - norminv(X.FDR); + X.YI = X.Sensitivity + X.Specificity - 1; % Youden Index % statistical significance test of Matthews' correlation coefficient NN = sum(H(:)); diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/inst/naninsttest.m new/nan-3.5.3/inst/naninsttest.m --- old/nan-3.5.2/inst/naninsttest.m 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/inst/naninsttest.m 2021-02-15 07:41:05.000000000 +0100 @@ -118,8 +118,7 @@ if exist('nanstd','file'), r(33,k)=k*(~isnan(nanstd(0))); end; - - %%% check mex files + try histo_mex([1:5]'); r(34,k)=0; @@ -144,6 +143,10 @@ if ~exist('train','file'), r(38,k)=k; end; + + if exist('ttest','file'), + r(39,k)=ttest([x,x,x],10); + end; end; % check if result is correct diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/inst/roc.m new/nan-3.5.3/inst/roc.m --- old/nan-3.5.2/inst/roc.m 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/inst/roc.m 2021-02-15 07:41:05.000000000 +0100 @@ -66,7 +66,7 @@ % return the optimal threshold for the respective measure. % RES.H_kappa: confusion matrix when Threshold of maximum Kappa is applied. % RES.H_{yi,acc,kappa,mcc,mi,f1,phi}: confusion matrix when threshold of -% optimum {...} is applied. +% optimum {...} is applied. Its structure is [TN, FN; FP; TP]. % % see also: AUC, PLOT, ROC % @@ -81,7 +81,7 @@ % (Eds.) G. Dornhege, J.R. Millan, T. Hinterberger, D.J. McFarland, K.-R.M??ller; % Towards Brain-Computer Interfacing, MIT Press, 2007, p.327-342 -% Copyright (c) 1997-2019 Alois Schloegl <alois.schlo...@gmail.com> +% Copyright (c) 1997-2021 Alois Schloegl <alois.schlo...@gmail.com> % This is part of the BIOSIG-toolbox http://biosig.sf.net/ % % This library is free software; you can redistribute it and/or @@ -202,9 +202,9 @@ %%% compute Cohen's kappa coefficient N = size(d,1); -%H = [TP,FN;FP,TN]; -p_i = [TP+FP,FN+TN];%sum(H,1); -pi_ = [TP+FN,FP+TN];%sum(H,2)'; +% H =[TN, FN; FP, TP] +p_i = [TP+FP, FN+TN]; +pi_ = [TP+FN, FP+TN]; pe = sum(p_i.*pi_,2)/(N*N); % estimate of change agreement kap = (ACC - pe) ./ (1 - pe); mcc = (TP .* TN - FN .* FP) ./ sqrt(prod( [p_i, pi_], 2)); @@ -274,7 +274,7 @@ % Cohen's kappa is best tested for borderline cases, like, few % samples only, or when multiple options are possible. % others are not that sophisticated. -[tmp,ix] = max(SEN+SPEC-1); +[RES.maxYI,ix] = max(SEN+SPEC-1); ix = min(ix,length(D)); RES.THRESHOLD.maxYI = D(ix); RES.THRESHOLD.maxYIix = ix; diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/src/Makefile.in new/nan-3.5.3/src/Makefile.in --- old/nan-3.5.2/src/Makefile.in 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/src/Makefile.in 2021-02-15 07:41:05.000000000 +0100 @@ -125,7 +125,7 @@ # -DMATLAB_DEFAULT_RELEASE=R2018a: Interleaved Complex MATLABMEX += -DMATLAB_DEFAULT_RELEASE=R2017b -CFLAGS := -fexceptions -fPIC -fno-omit-frame-pointer -pthread +CFLAGS += -fexceptions -fPIC -fno-omit-frame-pointer -pthread COPTIMFLAGS := -O -DNDEBUG CDEBUGFLAGS := -g INCLUDE := -I"$(MWROOT)/extern/include" -I"$(MWROOT)/simulink/include" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/src/configure.ac new/nan-3.5.3/src/configure.ac --- old/nan-3.5.2/src/configure.ac 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/src/configure.ac 2021-02-15 07:41:05.000000000 +0100 @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ([2.69]) -AC_INIT([nan-toolbox], [3.5.0], [alois.schlo...@gmail.com]) +AC_INIT([nan-toolbox], [3.5.3], [alois.schlo...@gmail.com]) AC_CONFIG_SRCDIR([train.c]) AC_CONFIG_HEADERS([config.h]) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.5.2/src/linear.cpp new/nan-3.5.3/src/linear.cpp --- old/nan-3.5.2/src/linear.cpp 2020-10-31 17:44:32.000000000 +0100 +++ new/nan-3.5.3/src/linear.cpp 2021-02-15 07:41:05.000000000 +0100 @@ -65,7 +65,7 @@ fputs(s,stdout); fflush(stdout); } -static void print_null(const char *s) {} +static void print_null(const char*) {} static void (*liblinear_print_string) (const char *) = &print_string_stdout; @@ -3073,7 +3073,7 @@ free(param->init_sol); } -const char *check_parameter(const problem *prob, const parameter *param) +const char *check_parameter(const problem*, const parameter *param) { if(param->eps <= 0) return "eps <= 0";