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stk >> STK, a Small Toolbox for Kriging

## Copyright Notice
##
##    Copyright (C) 2015-2021 CentraleSupelec
##    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
##               (https://github.com/stk-kriging/stk/)
##
##    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/>.

## Several reasons why we don't want to let certain functions
## appear in the INDEX (i.e., in the public API of STK)
##
##  1) Deprecation: these functions will be removed in future
##     versions of STK, no need to adertise them.
##
##  2) Internal: these functions are mostly intended for internal
##     use in STK. Although it might be occasionnaly useful for
##     advanced users to call them directly, they are not considered
##     as part of the public API and therefore not as stable as
##     public API functions. Use at your own risk.
##
##  3) Trivial overload: these functions provide the same functionality
##     as a corresponding "generic" function, with such a similar
##     behaviour that no documentation needs to be provided. For
##     instance, @stk_dataframe/abs is just a shortcut to avoid
##     writing abs (double (x)) or abs (x.data) when x is an
##     stk_dataframe object. No need to advertise such functions in
##     the INDEX.
##
##  4) Experimental features: not ready yet for use by everyone.
##

Core STK functions
## Why not group all these functions in the same folder ?
## Currently, some of them are in ./core/ and some others in ./utils/
 stk_model
 stk_model_update
 stk_make_matcov
 stk_predict
 stk_predict_leaveoneout
 stk_pmisclass
#stk_ortho_func              [deprecated]
#stk_cholcov                 [internal]
#stk_model_fixlm             [internal]
#stk_covmat_noise            [internal]
#stk_predict_                [internal]

Parameter estimation
 stk_param_estim
 stk_param_gls
 stk_param_init
 stk_param_init_lnv
 stk_param_relik
#stk_param_estim_optim           [internal]
#stk_param_getdefaultbounds      [internal]
#stk_param_getdefaultbounds_lnv  [internal]
#stk_param_init_remlgls          [internal]
#stk_get_optimizable_parameters  [internal]
#stk_set_optimizable_parameters  [internal]

Simulations
 stk_conditioning
 stk_generate_samplepaths
 stk_simulate_noise

## Base class for model objects
#@stk_model_/stk_model_                     [internal]
#@stk_model_/stk_predict_                   [internal]
#@stk_model_/stk_covmat_noise               [overload STK]
#@stk_model_/stk_get_input_data             [overload STK]
#@stk_model_/stk_get_output_data            [overload STK]
#@stk_model_/stk_get_prior_model            [overload STK]
#@stk_model_/stk_get_sample_size            [overload STK]
#@stk_model_/stk_get_observation_variances  [overload STK]
#@stk_model_/cat                            [overload base]
#@stk_model_/disp                           [overload base]
#@stk_model_/display                        [overload base]
#@stk_model_/get                            [overload base]
#@stk_model_/horzcat                        [overload base]
#@stk_model_/set                            [overload base]
#@stk_model_/subsasgn                       [overload base]
#@stk_model_/subsref                        [overload base]
#@stk_model_/vertcat                        [overload base]

Get/set model properties
 stk_get_input_data
 stk_get_output_data
 stk_get_prior_model
 stk_get_observation_variances
 stk_isnoisy
#stk_set_optimizable_model_parameters          [internal]
#stk_get_optimizable_model_parameters          [internal]
#stk_get_optimizable_noise_parameters          [internal]

Posterior model objects
 @stk_model_gpposterior/stk_model_gpposterior
 @stk_model_gpposterior/stk_predict_leaveoneout
 @stk_model_gpposterior/stk_model_update
#@stk_model_gpposterior/stk_covmat_noise                      [overload STK]
#@stk_model_gpposterior/stk_isnoisy                           [overload STK]
#@stk_model_gpposterior/stk_generate_samplepaths              [overload STK]
#@stk_model_gpposterior/stk_get_observation_variances         [overload STK]
#@stk_model_gpposterior/stk_get_optimizable_parameters        [overload STK]
#@stk_model_gpposterior/stk_set_optimizable_parameters        [overload STK]
#@stk_model_gpposterior/stk_get_optimizable_noise_parameters  [overload STK]
#@stk_model_gpposterior/stk_get_input_data                    [overload STK]
#@stk_model_gpposterior/stk_get_output_data                   [overload STK]
#@stk_model_gpposterior/stk_get_prior_model                   [overload STK]
#@stk_model_gpposterior/stk_get_sample_size                   [overload STK]
#@stk_model_gpposterior/stk_make_kreq                         [internal]
#@stk_model_gpposterior/stk_predict_                          [internal]
#@stk_model_gpposterior/stk_predict_leaveoneout_direct        [internal]
#@stk_model_gpposterior/disp                                  [overload base]
#@stk_model_gpposterior/fieldnames                            [overload base]
#@stk_model_gpposterior/get                                   [overload base]
#@stk_model_gpposterior/set                                   [overload base]

## The stk_kre_qr class -> not ready to be exposed
#@stk_kreq_qr/disp                   [overload base]
#@stk_kreq_qr/display                [overload base]
#@stk_kreq_qr/get                    [overload base]
#@stk_kreq_qr/linsolve               [overload base]
#@stk_kreq_qr/subsref                [overload base]
#@stk_kreq_qr/stk_kreq_qr            [internal]
#@stk_kreq_qr/stk_set_righthandside  [internal]
#@stk_kreq_qr/stk_squared_seminorm   [internal]

Model components: covariance functions
 stk_expcov_aniso
 stk_expcov_iso
 stk_gausscov_aniso
 stk_gausscov_iso
 stk_materncov32_aniso
 stk_materncov32_iso
 stk_materncov52_aniso
 stk_materncov52_iso
 stk_materncov_aniso
 stk_materncov_iso
 stk_sphcov_aniso
 stk_sphcov_iso
 stk_discretecov
#stk_noisecov        [deprecated]

Model components: radial basis functions
 stk_rbf_exponential
 stk_rbf_gauss
 stk_rbf_matern
 stk_rbf_matern32
 stk_rbf_matern52
 stk_rbf_spherical

## Note: stk_sf_* were previously considered as experimental
##  -> in principle, they can be removed at any time
#stk_sf_gausscorr    [deprecated]
#stk_sf_matern       [deprecated]
#stk_sf_matern32     [deprecated]
#stk_sf_matern52     [deprecated]

Model components: linear model objects
 @stk_lm_affine/stk_lm_affine
 @stk_lm_constant/stk_lm_constant
 @stk_lm_cubic/stk_lm_cubic
 @stk_lm_matrix/stk_lm_matrix
 @stk_lm_null/stk_lm_null
 @stk_lm_quadratic/stk_lm_quadratic
 stk_lm_polynomial
#@stk_lm_affine/feval       [overload base]
#@stk_lm_constant/feval     [overload base]
#@stk_lm_cubic/feval        [overload base]
#@stk_lm_matrix/feval       [overload base]
#@stk_lm_null/feval         [overload base]
#@stk_lm_quadratic/feval    [overload base]

## Model components: noise model objects
#@stk_gaussiannoise_/stk_gaussiannoise_                  [internal]
#@stk_gaussiannoise_/disp                                [overload base]
#@stk_gaussiannoise_/stk_covmat_noise                    [overload STK]
#@stk_gaussiannoise_/stk_isnoisy                         [overload STK]
#@stk_gaussiannoise_/stk_covmat                          [internal]
#@stk_gaussiannoise_/stk_predict_                        [internal]
#@stk_gaussiannoise_het0/stk_gaussiannoise_het0          [experimental]
#@stk_gaussiannoise_het0/stk_variance_eval               [experimental]
#@stk_gaussiannoise_het0/disp                            [overload base]
#@stk_gaussiannoise_het0/fieldnames                      [overload base]
#@stk_gaussiannoise_het0/get                             [overload base]
#@stk_gaussiannoise_het0/set                             [overload base]
#@stk_gaussiannoise_het0/stk_get_optimizable_parameters  [overload STK]
#@stk_gaussiannoise_het0/stk_param_getdefaultbounds      [overload STK]
#@stk_gaussiannoise_het0/stk_set_optimizable_parameters  [overload STK]

Design of experiments (non-sequential): sampling
 stk_sampling_halton_rr2
 stk_sampling_sobol
 stk_sampling_maximinlhs
 stk_sampling_nesteddesign
 stk_sampling_nestedlhs
 stk_sampling_olhs
 stk_sampling_randomlhs
 stk_sampling_randunif
 stk_sampling_regulargrid
 stk_sampling_vdc_rr2

Design of experiments (non-sequential): criteria
## note: some are in misc/design, others in misc/dist...
## Shouldn't they all be in sampling/criteria ?
 stk_filldist
#stk_filldist_discretized   [internal]
#stk_filldist_exact         [internal]
 stk_maxabscorr
 stk_mindist
 stk_phipcrit

Design of experiments (sequential): criteria
 stk_sampcrit_ei_eval
 stk_sampcrit_ehvi_eval
 stk_sampcrit_emmi_eval
 stk_sampcrit_akg_eval
 stk_distrib_normal_ei
 stk_distrib_student_ei

## Design of experiments (sequential): criterion objects

#@stk_function/stk_function          [experimental]
#@stk_function/disp                  [overload base]
#@stk_function/display               [overload base]
#@stk_function/get                   [overload base]
#@stk_function/horzcat               [overload base]
#@stk_function/subsasgn              [overload base]
#@stk_function/subsref               [overload base]
#@stk_function/vertcat               [overload base]
#@stk_function/feval                 [overload base]

#@stk_sampcrit_ei/stk_sampcrit_ei    [experimental]
#@stk_sampcrit_ei/disp               [overload base]
#@stk_sampcrit_ei/feval              [overload base]
#@stk_sampcrit_ei/get                [overload base]
#@stk_sampcrit_ei/set                [overload base]

#@stk_sampcrit_eqi/stk_sampcrit_eqi  [experimental]
#@stk_sampcrit_eqi/disp              [overload base]
#@stk_sampcrit_eqi/feval             [overload base]
#@stk_sampcrit_eqi/get               [overload base]
#@stk_sampcrit_eqi/set               [overload base]

#@stk_sampcrit_akg/stk_sampcrit_akg  [experimental]
#@stk_sampcrit_akg/disp              [overload base]
#@stk_sampcrit_akg/feval             [overload base]
#@stk_sampcrit_akg/get               [overload base]
#@stk_sampcrit_akg/set               [overload base]

Examples: kriging basics
 stk_example_kb01
 stk_example_kb01n
 stk_example_kb02
 stk_example_kb02n
 stk_example_kb03
#stk_example_kb04
 stk_example_kb05
 stk_example_kb06
 stk_example_kb07
 stk_example_kb08
 stk_example_kb09
 stk_example_kb10

Examples: design of experiments
 stk_example_doe01
 stk_example_doe02
 stk_example_doe03
 stk_example_doe04
 stk_example_doe05
 stk_example_doe06

Examples: miscellaneous
 stk_example_misc01
 stk_example_misc02
 stk_example_misc03
 stk_example_misc04
 stk_example_misc05

Examples: test functions, datasets, etc.
 stk_dataset_twobumps
 stk_testfun_borehole
 stk_testfun_braninhoo
 stk_testfun_goldsteinprice
 stk_testfun_twobumps
 stk_testcase_truss3
 stk_testfun_truss3_bb
 stk_testfun_truss3_vol

## Cf. misc/distrib/README
#stk_distrib_normal_cdf      [internal]
#stk_distrib_normal_pdf      [internal]
#stk_distrib_student_cdf     [internal]
#stk_distrib_student_pdf     [internal]
#stk_distrib_bivnorm_cdf     [internal]

## A first step towards supporting more than nomal priors...
#stk_distrib_logpdf          [internal]
#stk_distrib_logpdf_grad     [internal]

Miscellaneous: arrays
 stk_boundingbox
 stk_feval
 stk_get_sample_size
 stk_normalize
 stk_rescale
 @stk_dataframe/stk_dataframe
 @stk_factorialdesign/stk_factorialdesign
 @stk_factorialdesign/ndgrid
 @stk_hrect/stk_hrect
#stk_length                  [deprecated]

Miscellaneous: Pareto optimality
 stk_dominatedhv
 stk_isdominated
 stk_paretofind

Miscellaneous: validation of models
 stk_distrib_normal_crps
 stk_plot_histnormres
 stk_plot_predvsobs

#stk_commonsize              [internal]
#stk_sprintf                 [internal]
#stk_sprintf_colnames        [internal]
#stk_sprintf_rownames        [internal]
#stk_sprintf_sizetype        [internal]

#@stk_dataframe/stk_boundingbox           [overload STK]
#@stk_dataframe/stk_conditioning          [overload STK]
#@stk_dataframe/stk_get_sample_size       [overload STK]
#@stk_dataframe/stk_length                [deprecated]
#@stk_dataframe/stk_normalize             [overload STK]
#@stk_dataframe/stk_rescale               [overload STK]
#@stk_dataframe/apply                     [internal]
#@stk_dataframe/set_data                  [internal]
#@stk_dataframe/stk_sprintf               [internal]
#@stk_dataframe/stk_sprintf_colnames      [internal]
#@stk_dataframe/stk_sprintf_rownames      [internal]
#@stk_dataframe/stk_sprintf_sizetype      [internal]
#@stk_dataframe/abs                       [overload base]
#@stk_dataframe/acos                      [overload base]
#@stk_dataframe/acosd                     [overload base]
#@stk_dataframe/acosh                     [overload base]
#@stk_dataframe/asin                      [overload base]
#@stk_dataframe/asind                     [overload base]
#@stk_dataframe/asinh                     [overload base]
#@stk_dataframe/atan                      [overload base]
#@stk_dataframe/atand                     [overload base]
#@stk_dataframe/atanh                     [overload base]
#@stk_dataframe/and                       [overload base]
#@stk_dataframe/bsxfun                    [overload base]
#@stk_dataframe/cat                       [overload base]
#@stk_dataframe/cos                       [overload base]
#@stk_dataframe/cosd                      [overload base]
#@stk_dataframe/cosh                      [overload base]
#@stk_dataframe/ctranspose                [overload base]
#@stk_dataframe/diff                      [overload base]
#@stk_dataframe/disp                      [overload base]
#@stk_dataframe/display                   [overload base]
#@stk_dataframe/double                    [overload base]
#@stk_dataframe/end                       [overload base]
#@stk_dataframe/eq                        [overload base]
#@stk_dataframe/exp                       [overload base]
#@stk_dataframe/expm1                     [overload base]
#@stk_dataframe/fieldnames                [overload base]
#@stk_dataframe/find                      [overload base]
#@stk_dataframe/ge                        [overload base]
#@stk_dataframe/get                       [overload base]
#@stk_dataframe/gt                        [overload base]
#@stk_dataframe/horzcat                   [overload base]
#@stk_dataframe/isempty                   [overload base]
#@stk_dataframe/isfinite                  [overload base]
#@stk_dataframe/isinf                     [overload base]
#@stk_dataframe/ismember                  [overload base]
#@stk_dataframe/isnan                     [overload base]
#@stk_dataframe/ldivide                   [overload base]
#@stk_dataframe/le                        [overload base]
#@stk_dataframe/length                    [overload base]
#@stk_dataframe/log                       [overload base]
#@stk_dataframe/log10                     [overload base]
#@stk_dataframe/log1p                     [overload base]
#@stk_dataframe/log2                      [overload base]
#@stk_dataframe/logical                   [overload base]
#@stk_dataframe/lt                        [overload base]
#@stk_dataframe/max                       [overload base]
#@stk_dataframe/mean                      [overload base]
#@stk_dataframe/median                    [overload base]
#@stk_dataframe/min                       [overload base]
#@stk_dataframe/minus                     [overload base]
#@stk_dataframe/mode                      [overload base]
#@stk_dataframe/mrdivide                  [overload base]
#@stk_dataframe/mldivide                  [overload base]
#@stk_dataframe/mtimes                    [overload base]
#@stk_dataframe/ne                        [overload base]
#@stk_dataframe/not                       [overload base]
#@stk_dataframe/or                        [overload base]
#@stk_dataframe/openvar                   [overload base]
#@stk_dataframe/plot                      [overload base]
#@stk_dataframe/plotmatrix                [overload base]
#@stk_dataframe/plus                      [overload base]
#@stk_dataframe/power                     [overload base]
#@stk_dataframe/prod                      [overload base]
#@stk_dataframe/subsasgn                  [overload base]
#@stk_dataframe/subsref                   [overload base]
#@stk_dataframe/rdivide                   [overload base]
#@stk_dataframe/realpow                   [overload base]
#@stk_dataframe/reshape                   [overload base]
#@stk_dataframe/set                       [overload base]
#@stk_dataframe/sin                       [overload base]
#@stk_dataframe/sind                      [overload base]
#@stk_dataframe/sinh                      [overload base]
#@stk_dataframe/size                      [overload base]
#@stk_dataframe/sort                      [overload base]
#@stk_dataframe/sqrt                      [overload base]
#@stk_dataframe/quantile                  [overload base]
#@stk_dataframe/std                       [overload base]
#@stk_dataframe/sum                       [overload base]
#@stk_dataframe/tan                       [overload base]
#@stk_dataframe/tand                      [overload base]
#@stk_dataframe/tanh                      [overload base]
#@stk_dataframe/times                     [overload base]
#@stk_dataframe/transpose                 [overload base]
#@stk_dataframe/uminus                    [overload base]
#@stk_dataframe/unique                    [overload base]
#@stk_dataframe/uplus                     [overload base]
#@stk_dataframe/var                       [overload base]
#@stk_dataframe/vertcat                   [overload base]
#@stk_dataframe/xlim                      [overload base]
#@stk_dataframe/xor                       [overload base]
#@stk_dataframe/ylim                      [overload base]

#@stk_factorialdesign/contour               [overload base]
#@stk_factorialdesign/fieldnames            [overload base]
#@stk_factorialdesign/get                   [overload base]
#@stk_factorialdesign/ismember              [overload base]
#@stk_factorialdesign/mesh                  [overload base]
#@stk_factorialdesign/meshc                 [overload base]
#@stk_factorialdesign/meshz                 [overload base]
#@stk_factorialdesign/pcolor                [overload base]
#@stk_factorialdesign/set                   [overload base]
#@stk_factorialdesign/subsasgn              [overload base]
#@stk_factorialdesign/surf                  [overload base]
#@stk_factorialdesign/uminus                [overload base]
#@stk_factorialdesign/stk_boundingbox       [overload STK]
#@stk_factorialdesign/stk_normalize         [overload STK]
#@stk_factorialdesign/stk_rescale           [overload STK]
#@stk_factorialdesign/stk_dataframe         [overload STK]
#@stk_factorialdesign/stk_sprintf           [internal]
#@stk_factorialdesign/stk_sprintf_levels    [internal]

#@stk_hrect/axis             [overload base]
#@stk_hrect/disp             [overload base]
#@stk_hrect/display          [overload base]
#@stk_hrect/get              [overload base]
#@stk_hrect/horzcat          [overload base]
#@stk_hrect/ismember         [overload base]
#@stk_hrect/subsasgn         [overload base]
#@stk_hrect/subsref          [overload base]
#@stk_hrect/vertcat          [overload base]
#@stk_hrect/stk_boundingbox  [overload STK]
#@stk_hrect/stk_normalize    [overload STK]
#@stk_hrect/stk_rescale      [overload STK]
#@stk_hrect/stk_dataframe    [overload STK]

Miscellaneous: optimizers for parameter estimation
 stk_minimize_boxconstrained
 stk_minimize_unconstrained
 stk_optim_isavailable
 @stk_optim_fmincon/stk_optim_fmincon
#@stk_optim_fmincon/stk_minimize_boxconstrained    [overload STK]
 @stk_optim_fminsearch/stk_optim_fminsearch
#@stk_optim_fminsearch/stk_minimize_unconstrained  [overload STK]
#@stk_optim_fminsearch/stk_minimize_boxconstrained [overload STK]
 @stk_optim_octavesqp/stk_optim_octavesqp
#@stk_optim_octavesqp/stk_minimize_boxconstrained  [overload STK]
#@stk_optim_octavesqp/stk_minimize_unconstrained   [overload STK]
#stk_optim_testmin_box                             [internal]
#stk_optim_testmin_unc                             [internal]
#@stk_optim_optimizer_/stk_optim_optimizer_        [internal]
#@stk_optim_optimizer_/stk_optim_isavailable       [overload STK]

Miscellaneous: options, plots...
 stk_dist
 stk_halfpintl
 stk_init
 stk_legend
 stk_options_get
 stk_options_set
 stk_plot1d
#stk_plot_shadedci    [internal]
 stk_plot_probdom2d
 stk_version

Miscellaneous: unit tests
 stk_test
 stk_runtests

#stk_gpquadform  [experimental]

## Replacement for some base functions related to figures. Mostly for use
## in STK's examples, to keep consistent graphical options accross all
## examples. No need to let these appear in the INDEX.
#stk_axes             [internal]
#stk_figure           [internal]
#stk_plot_getaxesarg  [internal]
#stk_labels           [internal]
#stk_subplot          [internal]
#stk_title            [internal]
#stk_xlabel           [internal]
#stk_ylabel           [internal]
#stk_zlabel           [internal]

## error/warning
#stk_error                   [internal]
#stk_assert_box              [internal]
#stk_assert_no_duplicates    [internal]
#stk_assert_model_struct     [internal]
#stk_isequal_tolabs          [internal]
#stk_isequal_tolrel          [internal]
#stk_is_lhs                  [internal]
#stk_test_class              [internal]
#stk_test_dfbinaryop         [internal]
#stk_test_critgrad           [internal]

## misc/text
#stk_disp_examplewelcome         [internal]
#stk_disp_progress               [internal]
#stk_disp_isloose                [internal]
#stk_disp_getformat              [internal]
#stk_sprintf_colvect             [internal]
#stk_sprintf_colvect_fixedpoint  [internal]
#stk_sprintf_colvect_scientific  [internal]
#stk_sprintf_framed              [internal]

## (embryonic) parallelization engine
#@stk_parallel_engine_none/stk_parallel_engine_none      [experimental]
#@stk_parallel_engine_none/stk_parallel_feval            [experimental]
#@stk_parallel_engine_none/stk_parallel_stop             [experimental]
#@stk_parallel_engine_parfor/stk_parallel_engine_parfor  [experimental]
#@stk_parallel_engine_parfor/stk_parallel_feval          [experimental]
#@stk_parallel_engine_parfor/stk_parallel_stop           [experimental]
#stk_parallel_cutblocks                                  [experimental]
#stk_parallel_engine_get                                 [experimental]
#stk_parallel_engine_set                                 [experimental]
#stk_parallel_feval                                      [experimental]
#stk_parallel_start                                      [experimental]
#stk_parallel_stop                                       [experimental]