diff options
author | Julien Bect <julien.bect@centralesupelec.fr> | 2020-12-30 13:40:56 -0300 |
---|---|---|
committer | Rafael Laboissière <rafael@debian.org> | 2020-12-30 13:40:56 -0300 |
commit | e44858ef0a35474c27b84baca88299e8c219dd57 (patch) | |
tree | d8e9e5a44631b1c00f6c72fa8f78a0cc2b16935d | |
parent | bcb9ef9e2a9266aac21560f731dd32394b619b4b (diff) |
Remove the MOLE
Forwarded: not-needed
Last-Update: 2019-10-24
Remove the MOLE (Matlab/Octave Language Extensions), which is a set of
helper functions that make it possible to run the stk package in Matlab
and in older releases of Octave.
Last-Update: 2019-10-24
Gbp-Pq: Name 0002-Remove-the-MOLE.patch
-rw-r--r-- | inst/misc/mole/graphics_toolkit/graphics_toolkit.m | 69 | ||||
-rw-r--r-- | inst/misc/mole/isrow/isrow.m | 34 | ||||
-rw-r--r-- | inst/misc/mole/linsolve/linsolve.m | 141 | ||||
-rw-r--r-- | inst/misc/mole/quantile/quantile.m | 463 | ||||
-rw-r--r-- | inst/stk_init.m | 92 | ||||
-rw-r--r-- | post_install.m | 42 |
6 files changed, 0 insertions, 841 deletions
diff --git a/inst/misc/mole/graphics_toolkit/graphics_toolkit.m b/inst/misc/mole/graphics_toolkit/graphics_toolkit.m deleted file mode 100644 index 6e43015..0000000 --- a/inst/misc/mole/graphics_toolkit/graphics_toolkit.m +++ /dev/null @@ -1,69 +0,0 @@ -% GRAPHICS_TOOLKIT indicates which toolkit is assigned to new figures. -% -% This is a (partial) replacement for the graphics_toolkit function that is missing both -% from Matlab and from some old version f Octave. -% -% CALL: NAME = graphics_toolkit () -% -% returns: -% -% * the result of get (0, 'defaultfigure__backend__') if you're running an old version -% of Octave that does not have graphics_toolkit, -% -% * 'matlab-nojvm' if running Matlab without the Java Virtual Machine, -% -% * 'matlab-jvm' if running Matlab with the Java Virtual Machine. - -% Copyright Notice -% -% Copyright (C) 2013, 2014 SUPELEC -% -% Author: Julien Bect <julien.bect@centralesupelec.fr> - -% Copying Permission Statement -% -% This file is part of -% -% STK: a Small (Matlab/Octave) Toolbox for Kriging -% (http://sourceforge.net/projects/kriging) -% -% STK 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. -% -% STK is distributed in the hope that it will be useful, but WITHOUT -% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -% or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public -% License for more details. -% -% You should have received a copy of the GNU General Public License -% along with STK. If not, see <http://www.gnu.org/licenses/>. - -function name = graphics_toolkit () - -if exist ('OCTAVE_VERSION', 'builtin') == 5 % Octave - - try - % This should work on older versions of Octave, e.g., 3.2.4 - % (there was no notion of a 'toolkit' at the time, but if gnuplot - % is reported as the backend, then it is also the toolkit) - name = get (0, 'defaultfigure__backend__'); - catch - error ('Unable to determine which toolkit is being used.'); - end - -else % Matlab - - try - assert (usejava ('jvm')); - name = 'matlab-jvm'; - catch - name = 'matlab-nojvm'; - end - -end - -end % function - -%#ok<*CTCH> diff --git a/inst/misc/mole/isrow/isrow.m b/inst/misc/mole/isrow/isrow.m deleted file mode 100644 index 2b1b1b5..0000000 --- a/inst/misc/mole/isrow/isrow.m +++ /dev/null @@ -1,34 +0,0 @@ -% ISROW returns true for row vectors and false otherwise - -% Copyright Notice -% -% Copyright (C) 2014 SUPELEC -% -% Author: Julien Bect <julien.bect@centralesupelec.fr> - -% Copying Permission Statement -% -% This file is part of -% -% STK: a Small (Matlab/Octave) Toolbox for Kriging -% (http://sourceforge.net/projects/kriging) -% -% STK 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. -% -% STK is distributed in the hope that it will be useful, but WITHOUT -% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -% or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public -% License for more details. -% -% You should have received a copy of the GNU General Public License -% along with STK. If not, see <http://www.gnu.org/licenses/>. - -function b = isrow (x) - -n = length (x); -b = isequal (size (x), [1 n]); - -end % function diff --git a/inst/misc/mole/linsolve/linsolve.m b/inst/misc/mole/linsolve/linsolve.m deleted file mode 100644 index 078de06..0000000 --- a/inst/misc/mole/linsolve/linsolve.m +++ /dev/null @@ -1,141 +0,0 @@ -## Copyright (C) 2013 Nir Krakauer -## -## This program is free software; you can redistribute it and/or modify -## it under the terms of the GNU General Public License as published by -## the Free Software Foundation; either version 3 of the License, or -## (at your option) any later version. -## -## This program is distributed in the hope that it will be useful, -## but WITHOUT ANY WARRANTY; without even the implied warranty of -## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -## GNU General Public License for more details. -## -## You should have received a copy of the GNU General Public License -## along with this program; If not, see <http://www.gnu.org/licenses/>. - -## -*- texinfo -*- -## @deftypefn {Function File} {@var{x} =} linsolve (@var{A}, @var{b}) -## @deftypefnx {Function File} {@var{x} =} linsolve (@var{A}, @var{b}, @var{opts}) -## @deftypefnx {Function File} {[@var{x}, @var{R}] =} linsolve (@dots{}) -## Solve the linear system @code{A*x = b}. -## -## With no options, this function is equivalent to the left division operator -## @w{(@code{x = A \ b})} or the matrix-left-divide function -## @w{(@code{x = mldivide (A, b)})}. -## -## Octave ordinarily examines the properties of the matrix @var{A} and chooses -## a solver that best matches the matrix. By passing a structure @var{opts} -## to @code{linsolve} you can inform Octave directly about the matrix @var{A}. -## In this case Octave will skip the matrix examination and proceed directly -## to solving the linear system. -## -## @strong{Warning:} If the matrix @var{A} does not have the properties -## listed in the @var{opts} structure then the result will not be accurate -## AND no warning will be given. When in doubt, let Octave examine the matrix -## and choose the appropriate solver as this step takes little time and the -## result is cached so that it is only done once per linear system. -## -## Possible @var{opts} fields (set value to true/false): -## -## @table @asis -## @item LT -## @var{A} is lower triangular -## -## @item UT -## @var{A} is upper triangular -## -## @item UHESS -## @var{A} is upper Hessenberg (currently makes no difference) -## -## @item SYM -## @var{A} is symmetric or complex Hermitian (currently makes no difference) -## -## @item POSDEF -## @var{A} is positive definite -## -## @item RECT -## @var{A} is general rectangular (currently makes no difference) -## -## @item TRANSA -## Solve @code{A'*x = b} by @code{transpose (A) \ b} -## @end table -## -## The optional second output @var{R} is the inverse condition number of -## @var{A} (zero if matrix is singular). -## @seealso{mldivide, matrix_type, rcond} -## @end deftypefn - -## Author: Nir Krakauer <nkrakauer@ccny.cuny.edu> - -## STK notes: -## * This version of linsolve.m comes from revision b66f068e4468 of Octave's -## hg repository (changeset by Nir Krakauer on 2013-09-26, 09:38:51) -## * The only change that has been made is the introduction of a tolerance -## in the first assert of the first unit test, that's all ! - -function [x, R] = linsolve (A, b, opts) - - if (nargin < 2 || nargin > 3) - print_usage (); - endif - - if (! (isnumeric (A) && isnumeric (b))) - error ("linsolve: A and B must be numeric"); - endif - - ## Process any opts - if (nargin > 2) - if (! isstruct (opts)) - error ("linsolve: OPTS must be a structure"); - endif - trans_A = false; - if (isfield (opts, "TRANSA") && opts.TRANSA) - trans_A = true; - A = A'; - endif - if (isfield (opts, "POSDEF") && opts.POSDEF) - A = matrix_type (A, "positive definite"); - endif - if (isfield (opts, "LT") && opts.LT) - if (trans_A) - A = matrix_type (A, "upper"); - else - A = matrix_type (A, "lower"); - endif - endif - if (isfield (opts, "UT") && opts.UT) - if (trans_A) - A = matrix_type (A, "lower"); - else - A = matrix_type (A, "upper"); - endif - endif - endif - - x = A \ b; - - if (nargout > 1) - if (issquare (A)) - R = rcond (A); - else - R = 0; - endif - endif -endfunction # linsolve - - -%!test -%! n = 4; -%! A = triu (rand (n)); -%! x = rand (n, 1); -%! b = A' * x; -%! opts.UT = true; -%! opts.TRANSA = true; -%! assert (linsolve (A, b, opts), A' \ b, 1e-12); - -%!error linsolve () -%!error linsolve (1) -%!error linsolve (1,2,3) -%!error <A and B must be numeric> linsolve ({1},2) -%!error <A and B must be numeric> linsolve (1,{2}) -%!error <OPTS must be a structure> linsolve (1,2,3) diff --git a/inst/misc/mole/quantile/quantile.m b/inst/misc/mole/quantile/quantile.m deleted file mode 100644 index 1d21751..0000000 --- a/inst/misc/mole/quantile/quantile.m +++ /dev/null @@ -1,463 +0,0 @@ -% QUANTILE ... - -% Copyright Notice -% -% Copyright (C) 2013 SUPELEC -% -% Author: Julien Bect <julien.bect@centralesupelec.fr> -% -% The function comes from Octave 3.7.6+'s quantile.m, with minor -% modifications. The original copyright notice was: -% -% Copyright (C) 2008-2012 Ben Abbott and Jaroslav Hajek - -% Copying Permission Statement -% -% This file is part of -% -% STK: a Small (Matlab/Octave) Toolbox for Kriging -% (http://sourceforge.net/projects/kriging) -% -% STK 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. -% -% STK is distributed in the hope that it will be useful, but WITHOUT -% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -% or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public -% License for more details. -% -% You should have received a copy of the GNU General Public License -% along with STK. If not, see <http://www.gnu.org/licenses/>. - -% ## Copyright (C) 2008-2012 Ben Abbott and Jaroslav Hajek -% ## -% ## This file is part of Octave. -% ## -% ## Octave 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. -% ## -% ## Octave is distributed in the hope that it will be useful, but -% ## WITHOUT ANY WARRANTY; without even the implied warranty of -% ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -% ## General Public License for more details. -% ## -% ## You should have received a copy of the GNU General Public License -% ## along with Octave; see the file COPYING. If not, see -% ## <http://www.gnu.org/licenses/>. -% -% ## -*- texinfo -*- -% ## @deftypefn {Function File} {@var{q} =} quantile (@var{x}) -% ## @deftypefnx {Function File} {@var{q} =} quantile (@var{x}, @var{p}) -% ## @deftypefnx {Function File} {@var{q} =} quantile (@var{x}, @var{p}, @var{dim}) -% ## @deftypefnx {Function File} {@var{q} =} quantile (@var{x}, @var{p}, @var{dim}, @var{method}) -% ## For a sample, @var{x}, calculate the quantiles, @var{q}, corresponding to -% ## the cumulative probability values in @var{p}. All non-numeric values (NaNs) -% ## of @var{x} are ignored. -% ## -% ## If @var{x} is a matrix, compute the quantiles for each column and -% ## return them in a matrix, such that the i-th row of @var{q} contains -% ## the @var{p}(i)th quantiles of each column of @var{x}. -% ## -% ## If @var{p} is unspecified, return the quantiles for -% ## @code{[0.00 0.25 0.50 0.75 1.00]}. -% ## The optional argument @var{dim} determines the dimension along which -% ## the quantiles are calculated. If @var{dim} is omitted, and @var{x} is -% ## a vector or matrix, it defaults to 1 (column-wise quantiles). If -% ## @var{x} is an N-D array, @var{dim} defaults to the first non-singleton -% ## dimension. -% ## -% ## The methods available to calculate sample quantiles are the nine methods -% ## used by R (@url{http://www.r-project.org/}). The default value is -% ## @w{METHOD = 5}. -% ## -% ## Discontinuous sample quantile methods 1, 2, and 3 -% ## -% ## @enumerate 1 -% ## @item Method 1: Inverse of empirical distribution function. -% ## -% ## @item Method 2: Similar to method 1 but with averaging at discontinuities. -% ## -% ## @item Method 3: SAS definition: nearest even order statistic. -% ## @end enumerate -% ## -% ## Continuous sample quantile methods 4 through 9, where p(k) is the linear -% ## interpolation function respecting each methods' representative cdf. -% ## -% ## @enumerate 4 -% ## @item Method 4: p(k) = k / n. That is, linear interpolation of the -% ## empirical cdf. -% ## -% ## @item Method 5: p(k) = (k - 0.5) / n. That is a piecewise linear function -% ## where the knots are the values midway through the steps of the empirical -% ## cdf. -% ## -% ## @item Method 6: p(k) = k / (n + 1). -% ## -% ## @item Method 7: p(k) = (k - 1) / (n - 1). -% ## -% ## @item Method 8: p(k) = (k - 1/3) / (n + 1/3). The resulting quantile -% ## estimates are approximately median-unbiased regardless of the distribution -% ## of @var{x}. -% ## -% ## @item Method 9: p(k) = (k - 3/8) / (n + 1/4). The resulting quantile -% ## estimates are approximately unbiased for the expected order statistics if -% ## @var{x} is normally distributed. -% ## @end enumerate -% ## -% ## Hyndman and Fan (1996) recommend method 8. Maxima, S, and R -% ## (versions prior to 2.0.0) use 7 as their default. Minitab and SPSS -% ## use method 6. @sc{matlab} uses method 5. -% ## -% ## References: -% ## -% ## @itemize @bullet -% ## @item Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New -% ## S Language. Wadsworth & Brooks/Cole. -% ## -% ## @item Hyndman, R. J. and Fan, Y. (1996) Sample quantiles in -% ## statistical packages, American Statistician, 50, 361--365. -% ## -% ## @item R: A Language and Environment for Statistical Computing; -% ## @url{http://cran.r-project.org/doc/manuals/fullrefman.pdf}. -% ## @end itemize -% ## -% ## Examples: -% ## @c Set example in small font to prevent overfull line -% ## -% ## @smallexample -% ## @group -% ## x = randi (1000, [10, 1]); # Create empirical data in range 1-1000 -% ## q = quantile (x, [0, 1]); # Return minimum, maximum of distribution -% ## q = quantile (x, [0.25 0.5 0.75]); # Return quartiles of distribution -% ## @end group -% ## @end smallexample -% ## @seealso{prctile} -% ## @end deftypefn -% -% ## Author: Ben Abbott <bpabbott@mac.com> -% ## Description: Matlab style quantile function of a discrete/continuous distribution - -function q = quantile (x, p, dim, method) - -if nargin < 2, - p = []; -end - -if nargin < 3, - dim = 1; -end - -if nargin < 4, - % Use Matlab compatiblity mode - method = 5; -end - -if (~ (isnumeric (x) || islogical (x))) - error ('quantile: X must be a numeric vector or matrix'); -end - -if (isempty (p)) - p = [0.00 0.25, 0.50, 0.75, 1.00]; -end - -if (~ (isnumeric (p) && isvector (p))) - error ('quantile: P must be a numeric vector'); -end - -if (~ (isscalar (dim) && dim == fix (dim)) ... - || ~(1 <= dim && dim <= ndims (x))) - error ('quantile: DIM must be an integer and a valid dimension'); -end - -% Set the permutation vector. -perm = 1:ndims (x); -perm(1) = dim; -perm(dim) = 1; - -% Permute dim to the 1st index. -x = permute (x, perm); - -% Save the size of the permuted x N-d array. -sx = size (x); - -% Reshape to a 2-d array. -x = reshape (x, [sx(1), prod(sx(2:end))]); - -% Calculate the quantiles. -q = octave__quantile__ (x, p, method); - -% Return the shape to the original N-d array. -q = reshape (q, [numel(p), sx(2:end)]); - -% Permute the 1st index back to dim. -q = ipermute (q, perm); - -end % function - -%!test -%! p = 0.5; -%! x = sort (rand (11)); -%! q = quantile (x, p); -%! assert (isequal (q, x(6,:))); -%! x = x.'; -%! q = quantile (x, p, 2); -%! assert (isequal (q, x(:,6))); - -% Note: method 3 not available yet because Matlab doesn't have roundb() - -%!test -%! p = [0.00, 0.25, 0.50, 0.75, 1.00]; -%! x = [1; 2; 3; 4]; -%! a = [1.0000 1.0000 2.0000 3.0000 4.0000 -%! 1.0000 1.5000 2.5000 3.5000 4.0000 -%! 1.0000 1.0000 2.0000 3.0000 4.0000 -%! 1.0000 1.0000 2.0000 3.0000 4.0000 -%! 1.0000 1.5000 2.5000 3.5000 4.0000 -%! 1.0000 1.2500 2.5000 3.7500 4.0000 -%! 1.0000 1.7500 2.5000 3.2500 4.0000 -%! 1.0000 1.4167 2.5000 3.5833 4.0000 -%! 1.0000 1.4375 2.5000 3.5625 4.0000]; -%! for m = [1:2 4:9] -%! q = quantile (x, p, 1, m).'; -%! assert (stk_isequal_tolabs (q, a(m,:), 0.0001)); -%! end - -%!test -%! p = [0.00, 0.25, 0.50, 0.75, 1.00]; -%! x = [1; 2; 3; 4; 5]; -%! a = [1.0000 2.0000 3.0000 4.0000 5.0000 -%! 1.0000 2.0000 3.0000 4.0000 5.0000 -%! 1.0000 1.0000 2.0000 4.0000 5.0000 -%! 1.0000 1.2500 2.5000 3.7500 5.0000 -%! 1.0000 1.7500 3.0000 4.2500 5.0000 -%! 1.0000 1.5000 3.0000 4.5000 5.0000 -%! 1.0000 2.0000 3.0000 4.0000 5.0000 -%! 1.0000 1.6667 3.0000 4.3333 5.0000 -%! 1.0000 1.6875 3.0000 4.3125 5.0000]; -%! for m = [1:2 4:9] -%! q = quantile (x, p, 1, m).'; -%! assert (stk_isequal_tolabs (q, a(m,:), 0.0001)); -%! end - -%!test -%! p = [0.00, 0.25, 0.50, 0.75, 1.00]; -%! x = [1; 2; 5; 9]; -%! a = [1.0000 1.0000 2.0000 5.0000 9.0000 -%! 1.0000 1.5000 3.5000 7.0000 9.0000 -%! 1.0000 1.0000 2.0000 5.0000 9.0000 -%! 1.0000 1.0000 2.0000 5.0000 9.0000 -%! 1.0000 1.5000 3.5000 7.0000 9.0000 -%! 1.0000 1.2500 3.5000 8.0000 9.0000 -%! 1.0000 1.7500 3.5000 6.0000 9.0000 -%! 1.0000 1.4167 3.5000 7.3333 9.0000 -%! 1.0000 1.4375 3.5000 7.2500 9.0000]; -%! for m = [1:2 4:9] -%! q = quantile (x, p, 1, m).'; -%! assert (stk_isequal_tolabs (q, a(m,:), 0.0001)); -%! end - -%!test -%! p = [0.00, 0.25, 0.50, 0.75, 1.00]; -%! x = [1; 2; 5; 9; 11]; -%! a = [1.0000 2.0000 5.0000 9.0000 11.0000 -%! 1.0000 2.0000 5.0000 9.0000 11.0000 -%! 1.0000 1.0000 2.0000 9.0000 11.0000 -%! 1.0000 1.2500 3.5000 8.0000 11.0000 -%! 1.0000 1.7500 5.0000 9.5000 11.0000 -%! 1.0000 1.5000 5.0000 10.0000 11.0000 -%! 1.0000 2.0000 5.0000 9.0000 11.0000 -%! 1.0000 1.6667 5.0000 9.6667 11.0000 -%! 1.0000 1.6875 5.0000 9.6250 11.0000]; -%! for m = [1:2 4:9] -%! q = quantile (x, p, 1, m).'; -%! assert (stk_isequal_tolabs (q, a(m,:), 0.0001)); -%! end - -%!test -%! p = [0.00, 0.25, 0.50, 0.75, 1.00]; -%! x = [16; 11; 15; 12; 15; 8; 11; 12; 6; 10]; -%! a = [6.0000 10.0000 11.0000 15.0000 16.0000 -%! 6.0000 10.0000 11.5000 15.0000 16.0000 -%! 6.0000 8.0000 11.0000 15.0000 16.0000 -%! 6.0000 9.0000 11.0000 13.5000 16.0000 -%! 6.0000 10.0000 11.5000 15.0000 16.0000 -%! 6.0000 9.5000 11.5000 15.0000 16.0000 -%! 6.0000 10.2500 11.5000 14.2500 16.0000 -%! 6.0000 9.8333 11.5000 15.0000 16.0000 -%! 6.0000 9.8750 11.5000 15.0000 16.0000]; -%! for m = [1:2 4:9] -%! q = quantile (x, p, 1, m).'; -%! assert (stk_isequal_tolabs (q, a(m,:), 0.0001)); -%! end - -%!test -%! p = [0.00, 0.25, 0.50, 0.75, 1.00]; -%! x = [-0.58851; 0.40048; 0.49527; -2.551500; -0.52057; ... -%! -0.17841; 0.057322; -0.62523; 0.042906; 0.12337]; -%! a = [-2.551474 -0.588505 -0.178409 0.123366 0.495271 -%! -2.551474 -0.588505 -0.067751 0.123366 0.495271 -%! -2.551474 -0.625231 -0.178409 0.123366 0.495271 -%! -2.551474 -0.606868 -0.178409 0.090344 0.495271 -%! -2.551474 -0.588505 -0.067751 0.123366 0.495271 -%! -2.551474 -0.597687 -0.067751 0.192645 0.495271 -%! -2.551474 -0.571522 -0.067751 0.106855 0.495271 -%! -2.551474 -0.591566 -0.067751 0.146459 0.495271 -%! -2.551474 -0.590801 -0.067751 0.140686 0.495271]; -%! for m = [1:2 4:9] -%! q = quantile (x, p, 1, m).'; -%! assert (stk_isequal_tolabs (q, a(m,:), 0.0001)); -%! end - -%!test -%! p = 0.5; -%! x = [0.112600, 0.114800, 0.052100, 0.236400, 0.139300 -%! 0.171800, 0.727300, 0.204100, 0.453100, 0.158500 -%! 0.279500, 0.797800, 0.329600, 0.556700, 0.730700 -%! 0.428800, 0.875300, 0.647700, 0.628700, 0.816500 -%! 0.933100, 0.931200, 0.963500, 0.779600, 0.846100]; -%! tol = 0.00001; -%! x(5,5) = NaN; -%! assert (stk_isequal_tolabs ... -%! (quantile (x, p, 1), ... -%! [0.27950, 0.79780, 0.32960, 0.55670, 0.44460], tol)); -%! x(1,1) = NaN; -%! assert (stk_isequal_tolabs ... -%! (quantile (x, p, 1), ... -%! [0.35415, 0.79780, 0.32960, 0.55670, 0.44460], tol)); -%! x(3,3) = NaN; -%! assert (stk_isequal_tolabs ... -%! (quantile (x, p, 1), ... -%! [0.35415, 0.79780, 0.42590, 0.55670, 0.44460], tol)); - -%!test -%! sx = [2, 3, 4]; -%! x = rand (sx); -%! dim = 2; -%! p = 0.5; -%! yobs = quantile (x, p, dim); -%! yexp = median (x, dim); -%! assert (isequal (yobs, yexp)); - -%% Test input validation -%!error quantile () -%!error quantile (1, 2, 3, 4, 5) -%!error quantile (['A'; 'B'], 10) -%!error quantile (1:10, [true, false]) -%!error quantile (1:10, ones (2,2)) -%!error quantile (1, 1, 1.5) -%!error quantile (1, 1, 0) -%!error quantile (1, 1, 3) -%!error quantile ((1:5)', 0.5, 1, 0) -%!error quantile ((1:5)', 0.5, 1, 10) - -% ## For the cumulative probability values in @var{p}, compute the -% ## quantiles, @var{q} (the inverse of the cdf), for the sample, @var{x}. -% ## -% ## The optional input, @var{method}, refers to nine methods available in R -% ## (http://www.r-project.org/). The default is @var{method} = 7. -% ## @seealso{prctile, quantile, statistics} -% -% ## Author: Ben Abbott <bpabbott@mac.com> -% ## Vectorized version: Jaroslav Hajek <highegg@gmail.com> -% ## Description: Quantile function of empirical samples - -function inv = octave__quantile__ (x, p, method) - -if (isinteger (x) || islogical (x)) - x = double (x); -end - -% set shape of quantiles to column vector. -p = p(:); - -% Save length and set shape of samples. -% FIXME: does sort guarantee that NaN's come at the end? -x = sort (x); -m = sum (~ isnan (x)); -[xr, xc] = size (x); - -% Initialize output values. -inv = Inf (class (x)) * (-(p < 0) + (p > 1)); -inv = repmat (inv, 1, xc); - -% Do the work. -k = find ((p >= 0) & (p <= 1)); -if (any (k)) - n = length (k); - p = p(k); - % Special case of 1 row. - if (xr == 1) - inv(k,:) = repmat (x, n, 1); - return; - end - - % The column-distribution indices. - pcd = kron (ones (n, 1), xr*(0:xc-1)); - mm = kron (ones (n, 1), m); - switch (method) - case {1, 2, 3} - switch (method) - case 1 - p = max (ceil (kron (p, m)), 1); - inv(k,:) = x(p + pcd); - - case 2 - p = kron (p, m); - p_lr = max (ceil (p), 1); - p_rl = min (floor (p + 1), mm); - inv(k,:) = (x(p_lr + pcd) + x(p_rl + pcd))/2; - - case 3 - % Used by SAS, method PCTLDEF=2. - % http://support.sas.com/onlinedoc/913/getDoc/en/statug.hlp/stdize_sect14.htm - t = max (kron (p, m), 1); - t = roundb (t); - inv(k,:) = x(t + pcd); - end - - otherwise - switch (method) - case 4 - p = kron (p, m); - - case 5 - % Used by Matlab. - p = kron (p, m) + 0.5; - - case 6 - % Used by Minitab and SPSS. - p = kron (p, m+1); - - case 7 - % Used by S and R. - p = kron (p, m-1) + 1; - - case 8 - % Median unbiased. - p = kron (p, m+1/3) + 1/3; - - case 9 - % Approximately unbiased respecting order statistics. - p = kron (p, m+0.25) + 0.375; - - otherwise - error ('quantile: Unknown METHOD, ''%d''', method); - end - - % Duplicate single values. - imm1 = (mm == 1); - x(2,imm1) = x(1,imm1); - - % Interval indices. - pi = max (min (floor (p), mm-1), 1); - pr = max (min (p - pi, 1), 0); - pi = pi + pcd; - inv(k,:) = (1-pr) .* x(pi) + pr .* x(pi+1); - end -end - -end % function diff --git a/inst/stk_init.m b/inst/stk_init.m index 2fe55c1..937f308 100644 --- a/inst/stk_init.m +++ b/inst/stk_init.m @@ -53,9 +53,6 @@ switch command case 'pkg_unload' stk_init__pkg_unload (root); - case 'prune_mole' - stk_init__config_mole (root, false, true); % prune, but do not add to path - case 'clear_persistents' % Note: this implies munlock stk_init__clear_persistents (); @@ -181,9 +178,6 @@ end % Add STK folders to the path addpath (path{:}); -% Selectively add MOLE subdirectories to compensate for missing functions -stk_init__config_mole (root, true, false); % (add to path, but do not prune) - end % function @@ -272,89 +266,3 @@ s = strrep (s, '+', '\+'); s = strrep (s, '.', '\.'); end % function - - -function stk_init__config_mole (root, do_addpath, prune_unused) - -mole_dir = fullfile (root, 'misc', 'mole'); -isoctave = (exist ('OCTAVE_VERSION', 'builtin') == 5); - -if isoctave - recursive_rmdir_state = confirm_recursive_rmdir (0); -end - -opts = {root, mole_dir, do_addpath, prune_unused}; - -% Provide missing octave functions for Matlab users -% TODO: extract functions that are REALLY needed in separate directories -% and get rid of the others ! -if (exist ('OCTAVE_VERSION', 'builtin') ~= 5) % if Matlab - if do_addpath - addpath (fullfile (mole_dir, 'matlab')); - end -elseif prune_unused - rmdir (fullfile (mole_dir, 'matlab'), 's'); -end - -% graphics_toolkit -% * For Octave users: graphics_toolkit is missing in some old version of Octave -% * For Matlab users: there is no function named graphics_toolkit in Matlab. -% Our implementation returns either 'matlab-jvm' or 'matlab-nojvm'. -install_mole_function ('graphics_toolkit', opts{:}); - -% isrow -% * For Octave users: ? -% * For Matlab users: missing in R2007a -install_mole_function ('isrow', opts{:}); - -% linsolve -% * For Octave users: linsolve has been missing in Octave for a long time -% (up to 3.6.4) -% * For Matlab users: ? -install_mole_function ('linsolve', opts{:}); - -% quantile -% * For Octave users: ? -% * For Matlab users: quantile is missing from Matlab itself, but it provided -% by the Statistics toolbox if you're rich enough to afford it. -install_mole_function ('quantile', opts{:}); - -% cleanup -if isoctave - confirm_recursive_rmdir (recursive_rmdir_state); -end - -end % function - - -function install_mole_function (funct_name, ... - root, mole_dir, do_addpath, prune_unused) - -function_dir = fullfile (mole_dir, funct_name); - -w = which (funct_name); - -if (isempty (w)) || (~ isempty (strfind (w, root))) % if the function is absent - - function_mfile = fullfile (function_dir, [funct_name '.m']); - - if exist (function_dir, 'dir') && exist (function_mfile, 'file') - - % fprintf ('[MOLE] Providing function %s\n', function_name); - if do_addpath - addpath (function_dir); - end - - else - - warning (sprintf ('[MOLE] Missing function: %s\n', funct_name)); - - end - -elseif prune_unused && (exist (function_dir, 'dir')) - - rmdir (function_dir, 's'); - -end - -end % function diff --git a/post_install.m b/post_install.m deleted file mode 100644 index 8e6ee99..0000000 --- a/post_install.m +++ /dev/null @@ -1,42 +0,0 @@ -# POST_INSTALL is run after the installation of the package - -# Copyright Notice -# -# Copyright (C) 2014 SUPELEC -# Copyright (C) 2015 CentraleSupelec -# -# Author: Julien Bect <julien.bect@centralesupelec.fr> - -# Copying Permission Statement -# -# This file is part of -# -# STK: a Small (Matlab/Octave) Toolbox for Kriging -# (http://sourceforge.net/projects/kriging) -# -# STK 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. -# -# STK is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public -# License for more details. -# -# You should have received a copy of the GNU General Public License -# along with STK. If not, see <http://www.gnu.org/licenses/>. - -function post_install (desc) - - here = pwd (); - - # Prune unused functions from the MOLE - unwind_protect - cd (desc.dir); - stk_init prune_mole - unwind_protect_cleanup - cd (here); - end_unwind_protect - -endfunction |