stk >> STK, a Small Toolbox for Kriging

## Copyright Notice
##
##    Copyright (C) 2015-2017 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
##               (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/>.

## 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_conditioning
 stk_generate_samplepaths
 stk_isnoisy
#stk_ortho_func              [deprecated]
#stk_cholcov                 [internal]
#stk_model_fixlm             [internal]

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

Posterior model objects
 @stk_model_gpposterior/stk_model_gpposterior
 @stk_model_gpposterior/stk_predict
 @stk_model_gpposterior/stk_predict_leaveoneout
 @stk_model_gpposterior/stk_model_update
 @stk_model_gpposterior/get_input_data
 @stk_model_gpposterior/get_output_data
 @stk_model_gpposterior/get_prior_model
#@stk_model_gpposterior/stk_isnoisy                     [overload STK]
#@stk_model_gpposterior/stk_generate_samplepaths        [overload STK]
#@stk_model_gpposterior/stk_make_kreq                   [internal]
#@stk_model_gpposterior/stk_predict_leaveoneout_direct  [internal]
#@stk_model_gpposterior/disp                            [overload base]
#@stk_model_gpposterior/display                         [overload base]
#@stk_model_gpposterior/fieldnames                      [overload base]
#@stk_model_gpposterior/get                             [overload base]
#@stk_model_gpposterior/isequal                         [overload base]
#@stk_model_gpposterior/set                             [overload base]
#@stk_model_gpposterior/subsasgn                        [overload base]
#@stk_model_gpposterior/subsref                         [overload base]
#@stk_model_gpposterior/horzcat                         [overload base]
#@stk_model_gpposterior/vertcat                         [overload base]

## Prior models are currently represented by structures
#@struct/get_input_data                        [internal]
#@struct/get_output_data                       [internal]
#@struct/get_prior_model                       [internal]

## 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/isequal                [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]
#@stk_kreq_qr/stk_update             [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_noisecov
 stk_discretecov

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_affine/isequal     [overload base]
#@stk_lm_constant/feval     [overload base]
#@stk_lm_constant/isequal   [overload base]
#@stk_lm_cubic/feval        [overload base]
#@stk_lm_cubic/isequal      [overload base]
#@stk_lm_matrix/feval       [overload base]
#@stk_lm_matrix/isequal     [overload base]
#@stk_lm_null/feval         [overload base]
#@stk_lm_null/isequal       [overload base]
#@stk_lm_quadratic/feval    [overload base]
#@stk_lm_quadratic/isequal  [overload base]

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): criterions
## note: some are in misc/design, others in misc/dist...
## Shouldn't they all be in sampling/criterions ?
 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  [experi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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