stk >> STK, a Small Toolbox for Kriging

## 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. A necessary (but not sufficient) condition
##     for a function to be called "internal" is that it should not
##     be used in any of the stk_example_* scripts. 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.
##

Kriging: 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_make_matcov
 stk_predict
 stk_conditioning
 stk_generate_samplepaths
#stk_ortho_func              [deprecated]
#stk_cholcov                 [internal]

Kriging: Parameter estimation
 stk_param_estim
#stk_param_getdefaultbounds  [internal]
 stk_param_gls
 stk_param_init
 stk_param_init_lnv
 stk_param_relik

## The stk_kre_qr class -> not ready to be exposed
#@stk_kreq_qr/get                    [internal]
#@stk_kreq_qr/isequal                [internal]
#@stk_kreq_qr/linsolve               [internal]
#@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]
#@stk_kreq_qr/subsref                [internal]

Kriging: Covariance functions
 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_noisecov
 stk_discretecov

## The prefix 'sf' for 'special functions' is not appropriate, since the
## expression 'special function' refers to specific rather specific in the
## traditional math vocabulary... Because of that, these functions are
## likely to be renamed in future versions of STK. Until then, let us
## consider them as "internal" (they are never used directly in any of the
## example scripts)
#stk_sf_gausscorr    [internal]
#stk_sf_matern       [internal]
#stk_sf_matern32     [internal]
#stk_sf_matern52     [internal]

## The use of stk_lm_* objects is currently considered as an experimental
## feature. It is not advertised in any of the example scripts. Moreover,
## it requires to set model.order to NaN, a "cheat code" feature which
## is very weakly documented (only in stk_example_misc03). stk_lm_*
## should become the standard way of of defining the "linear part" of a
## model in the next major release of STK.
#@stk_lm_affine/stk_lm_affine          [experimental]
#@stk_lm_affine/feval                  [experimental]
#@stk_lm_constant/stk_lm_constant      [experimental]
#@stk_lm_constant/feval                [experimental]
#@stk_lm_cubic/stk_lm_cubic            [experimental]
#@stk_lm_cubic/feval                   [experimental]
#@stk_lm_matrix/stk_lm_matrix          [experimental]
#@stk_lm_matrix/feval                  [experimental]
#@stk_lm_null/stk_lm_null              [experimental]
#@stk_lm_null/feval                    [experimental]
#@stk_lm_quadratic/stk_lm_quadratic    [experimental]
#@stk_lm_quadratic/feval               [experimental]

Design of experiments (non-sequential): sampling
 stk_sampling_halton_rr2
 stk_sampling_maximinlhs
 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): expected improvement
 stk_distrib_normal_ei
 stk_distrib_student_ei

Examples: kriging basics
 stk_example_kb01
 stk_example_kb02
 stk_example_kb03
 stk_example_kb04
 stk_example_kb05
 stk_example_kb06
 stk_example_kb07
 stk_example_kb08
 stk_example_kb09

Examples: design of experiments
 stk_example_doe01
 stk_example_doe02
 stk_example_doe03

Examples: miscellaneous
 stk_example_misc01
 stk_example_misc02
 stk_example_misc03
 stk_example_misc04

#stk_testfun_braninhoo
#stk_testfun_goldsteinprice

## 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]

Miscellaneous: arrays
 stk_boundingbox
 stk_feval
 stk_isdominated
 stk_length
 stk_normalize
 stk_paretofind
 stk_rescale
 @stk_dataframe/stk_dataframe
 @stk_factorialdesign/stk_factorialdesign
 @stk_factorialdesign/ndgrid
 @stk_hrect/stk_hrect

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

#@cell/stk_sprintf_sizetype  [internal]

## Those are for legacy support of .a data structures
## (will be completely removed in the 3.x series)
#@struct/double
#@struct/stk_boundingbox
#@struct/stk_length

#@stk_dataframe/stk_boundingbox           [overload STK]
#@stk_dataframe/stk_conditioning          [overload STK]
#@stk_dataframe/stk_generate_samplepaths  [overload STK]
#@stk_dataframe/stk_length                [overload STK]
#@stk_dataframe/stk_normalize             [overload STK]
#@stk_dataframe/stk_rescale               [overload STK]
#@stk_dataframe/apply                     [internal]
#@stk_dataframe/stk_sprintf               [internal]
#@stk_dataframe/stk_sprintf_colnames      [internal]
#@stk_dataframe/stk_sprintf_info          [internal]
#@stk_dataframe/stk_sprintf_rownames      [internal]
#@stk_dataframe/stk_sprintf_sizetype      [internal]
#@stk_dataframe/abs                       [overload base]
#@stk_dataframe/and                       [overload base]
#@stk_dataframe/bsxfun                    [overload base]
#@stk_dataframe/cat                       [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/fieldnames                [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/isequal                   [overload base]
#@stk_dataframe/ismember                  [overload base]
#@stk_dataframe/ldivide                   [overload base]
#@stk_dataframe/le                        [overload base]
#@stk_dataframe/length                    [overload base]
#@stk_dataframe/lt                        [overload base]
#@stk_dataframe/ne                        [overload base]
#@stk_dataframe/or                        [overload base]
#@stk_dataframe/plot                      [overload base]
#@stk_dataframe/subsasgn                  [overload base]
#@stk_dataframe/subsref                   [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/mtimes                    [overload base]
#@stk_dataframe/plus                      [overload base]
#@stk_dataframe/power                     [overload base]
#@stk_dataframe/prod                      [overload base]
#@stk_dataframe/rdivide                   [overload base]
#@stk_dataframe/realpow                   [overload base]
#@stk_dataframe/reshape                   [overload base]
#@stk_dataframe/set                       [overload base]
#@stk_dataframe/size                      [overload base]
#@stk_dataframe/sort                      [overload base]
#@stk_dataframe/quantile                  [overload base]
#@stk_dataframe/std                       [overload base]
#@stk_dataframe/sum                       [overload base]
#@stk_dataframe/times                     [overload base]
#@stk_dataframe/transpose                 [overload base]
#@stk_dataframe/uminus                    [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/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_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]

Miscellaneous: options, plots...
 stk_dist
 stk_init
 stk_options_get
 stk_options_set
 stk_plot1d
#stk_plot2d           [deprecated]
#stk_plot_shadedci    [internal]
 stk_select_optimizer
 stk_version

#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_get_axis_arg  [internal]
#stk_labels        [internal]
#stk_subplot       [internal]
#stk_title         [internal]
#stk_xlabel        [internal]
#stk_ylabel        [internal]
#stk_zlabel        [internal]

## error/warning
#stk_error [internal, not for public use]
##stk_warning does not exist yet, but it should (?)

## misc/text
#stk_disp_examplewelcome
#stk_disp_progress
#stk_sprintf_colvect
#stk_sprintf_colvect_fixedpoint
#stk_sprintf_colvect_scientific
#stk_sprintf_framed

## testing STK
#stk_assert_box       [internal]
#stk_isequal_tolabs
#stk_isequal_tolrel
#stk_is_lhs
#stk_test_dfbinaryop

## (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]
