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102
doc/GPy.core.parameterization.rst Normal file
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GPy.core.parameterization package
=================================
Submodules
----------
GPy.core.parameterization.domains module
----------------------------------------
.. automodule:: GPy.core.parameterization.domains
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.index_operations module
-------------------------------------------------
.. automodule:: GPy.core.parameterization.index_operations
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.lists_and_dicts module
------------------------------------------------
.. automodule:: GPy.core.parameterization.lists_and_dicts
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.observable_array module
-------------------------------------------------
.. automodule:: GPy.core.parameterization.observable_array
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.param module
--------------------------------------
.. automodule:: GPy.core.parameterization.param
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.parameter_core module
-----------------------------------------------
.. automodule:: GPy.core.parameterization.parameter_core
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.parameterized module
----------------------------------------------
.. automodule:: GPy.core.parameterization.parameterized
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.priors module
---------------------------------------
.. automodule:: GPy.core.parameterization.priors
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.ties_and_remappings module
----------------------------------------------------
.. automodule:: GPy.core.parameterization.ties_and_remappings
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.transformations module
------------------------------------------------
.. automodule:: GPy.core.parameterization.transformations
:members:
:undoc-members:
:show-inheritance:
GPy.core.parameterization.variational module
--------------------------------------------
.. automodule:: GPy.core.parameterization.variational
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.core.parameterization
:members:
:undoc-members:
:show-inheritance:

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doc/GPy.core.rst
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GPy.core package GPy.core package
================ ================
Subpackages
-----------
.. toctree::
GPy.core.parameterization
Submodules Submodules
---------- ----------
GPy.core.domains module
-----------------------
.. automodule:: GPy.core.domains
:members:
:undoc-members:
:show-inheritance:
GPy.core.fitc module
--------------------
.. automodule:: GPy.core.fitc
:members:
:undoc-members:
:show-inheritance:
GPy.core.gp module GPy.core.gp module
------------------ ------------------
@ -28,14 +19,6 @@ GPy.core.gp module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.core.gp_base module
-----------------------
.. automodule:: GPy.core.gp_base
:members:
:undoc-members:
:show-inheritance:
GPy.core.mapping module GPy.core.mapping module
----------------------- -----------------------
@ -52,22 +35,6 @@ GPy.core.model module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.core.parameterized module
-----------------------------
.. automodule:: GPy.core.parameterized
:members:
:undoc-members:
:show-inheritance:
GPy.core.priors module
----------------------
.. automodule:: GPy.core.priors
:members:
:undoc-members:
:show-inheritance:
GPy.core.sparse_gp module GPy.core.sparse_gp module
------------------------- -------------------------
@ -76,6 +43,14 @@ GPy.core.sparse_gp module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.core.sparse_gp_mpi module
-----------------------------
.. automodule:: GPy.core.sparse_gp_mpi
:members:
:undoc-members:
:show-inheritance:
GPy.core.svigp module GPy.core.svigp module
--------------------- ---------------------
@ -84,10 +59,10 @@ GPy.core.svigp module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.core.transformations module GPy.core.symbolic module
------------------------------- ------------------------
.. automodule:: GPy.core.transformations .. automodule:: GPy.core.symbolic
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:

16
doc/GPy.examples.rst
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@ -12,6 +12,14 @@ GPy.examples.classification module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.examples.coreg_example module
---------------------------------
.. automodule:: GPy.examples.coreg_example
:members:
:undoc-members:
:show-inheritance:
GPy.examples.dimensionality_reduction module GPy.examples.dimensionality_reduction module
-------------------------------------------- --------------------------------------------
@ -20,6 +28,14 @@ GPy.examples.dimensionality_reduction module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.examples.non_gaussian module
--------------------------------
.. automodule:: GPy.examples.non_gaussian
:members:
:undoc-members:
:show-inheritance:
GPy.examples.regression module GPy.examples.regression module
------------------------------ ------------------------------

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GPy.inference.latent_function_inference package
===============================================
Submodules
----------
GPy.inference.latent_function_inference.dtc module
--------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.dtc
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.exact_gaussian_inference module
-----------------------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.exact_gaussian_inference
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.expectation_propagation module
----------------------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.expectation_propagation
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.expectation_propagation_dtc module
--------------------------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.expectation_propagation_dtc
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.fitc module
---------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.fitc
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.laplace module
------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.laplace
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.posterior module
--------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.posterior
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.var_dtc module
------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.var_dtc
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.var_dtc_gpu module
----------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.var_dtc_gpu
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.var_dtc_parallel module
---------------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.var_dtc_parallel
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.inference.latent_function_inference
:members:
:undoc-members:
:show-inheritance:

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GPy.inference.optimization package
==================================
Submodules
----------
GPy.inference.optimization.BayesOpt module
------------------------------------------
.. automodule:: GPy.inference.optimization.BayesOpt
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.conjugate_gradient_descent module
------------------------------------------------------------
.. automodule:: GPy.inference.optimization.conjugate_gradient_descent
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.gradient_descent_update_rules module
---------------------------------------------------------------
.. automodule:: GPy.inference.optimization.gradient_descent_update_rules
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.hmc module
-------------------------------------
.. automodule:: GPy.inference.optimization.hmc
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.optimization module
----------------------------------------------
.. automodule:: GPy.inference.optimization.optimization
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.samplers module
------------------------------------------
.. automodule:: GPy.inference.optimization.samplers
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.scg module
-------------------------------------
.. automodule:: GPy.inference.optimization.scg
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization.sgd module
-------------------------------------
.. automodule:: GPy.inference.optimization.sgd
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.inference.optimization
:members:
:undoc-members:
:show-inheritance:

54
doc/GPy.inference.rst
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@ -1,57 +1,13 @@
GPy.inference package GPy.inference package
===================== =====================
Submodules Subpackages
---------- -----------
GPy.inference.conjugate_gradient_descent module .. toctree::
-----------------------------------------------
.. automodule:: GPy.inference.conjugate_gradient_descent
:members:
:undoc-members:
:show-inheritance:
GPy.inference.gradient_descent_update_rules module
--------------------------------------------------
.. automodule:: GPy.inference.gradient_descent_update_rules
:members:
:undoc-members:
:show-inheritance:
GPy.inference.optimization module
---------------------------------
.. automodule:: GPy.inference.optimization
:members:
:undoc-members:
:show-inheritance:
GPy.inference.samplers module
-----------------------------
.. automodule:: GPy.inference.samplers
:members:
:undoc-members:
:show-inheritance:
GPy.inference.scg module
------------------------
.. automodule:: GPy.inference.scg
:members:
:undoc-members:
:show-inheritance:
GPy.inference.sgd module
------------------------
.. automodule:: GPy.inference.sgd
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference
GPy.inference.optimization
Module contents Module contents
--------------- ---------------

27
doc/GPy.kern.rst
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@ -1,33 +1,6 @@
GPy.kern package GPy.kern package
================ ================
Subpackages
-----------
.. toctree::
GPy.kern.parts
Submodules
----------
GPy.kern.constructors module
----------------------------
.. automodule:: GPy.kern.constructors
:members:
:undoc-members:
:show-inheritance:
GPy.kern.kern module
--------------------
.. automodule:: GPy.kern.kern
:members:
:undoc-members:
:show-inheritance:
Module contents Module contents
--------------- ---------------

113
doc/GPy.likelihoods.rst
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@ -1,28 +1,29 @@
GPy.likelihoods package GPy.likelihoods package
======================= =======================
Subpackages
-----------
.. toctree::
GPy.likelihoods.noise_models
Submodules Submodules
---------- ----------
GPy.likelihoods.ep module GPy.likelihoods.bernoulli module
------------------------- --------------------------------
.. automodule:: GPy.likelihoods.ep .. automodule:: GPy.likelihoods.bernoulli
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.likelihoods.ep_mixed_noise module GPy.likelihoods.exponential module
------------------------------------- ----------------------------------
.. automodule:: GPy.likelihoods.ep_mixed_noise .. automodule:: GPy.likelihoods.exponential
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.gamma module
----------------------------
.. automodule:: GPy.likelihoods.gamma
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
@ -35,14 +36,6 @@ GPy.likelihoods.gaussian module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.likelihoods.gaussian_mixed_noise module
-------------------------------------------
.. automodule:: GPy.likelihoods.gaussian_mixed_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.likelihood module GPy.likelihoods.likelihood module
--------------------------------- ---------------------------------
@ -51,10 +44,82 @@ GPy.likelihoods.likelihood module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.likelihoods.noise_model_constructors module GPy.likelihoods.link_functions module
----------------------------------------------- -------------------------------------
.. automodule:: GPy.likelihoods.noise_model_constructors .. automodule:: GPy.likelihoods.link_functions
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.mixed_noise module
----------------------------------
.. automodule:: GPy.likelihoods.mixed_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.negative_binomial module
----------------------------------------
.. automodule:: GPy.likelihoods.negative_binomial
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.ordinal module
------------------------------
.. automodule:: GPy.likelihoods.ordinal
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.poisson module
------------------------------
.. automodule:: GPy.likelihoods.poisson
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.skew_exponential module
---------------------------------------
.. automodule:: GPy.likelihoods.skew_exponential
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.skew_normal module
----------------------------------
.. automodule:: GPy.likelihoods.skew_normal
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.sstudent_t module
---------------------------------
.. automodule:: GPy.likelihoods.sstudent_t
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.student_t module
--------------------------------
.. automodule:: GPy.likelihoods.student_t
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.symbolic module
-------------------------------
.. automodule:: GPy.likelihoods.symbolic
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:

16
doc/GPy.mappings.rst
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@ -4,6 +4,14 @@ GPy.mappings package
Submodules Submodules
---------- ----------
GPy.mappings.additive module
----------------------------
.. automodule:: GPy.mappings.additive
:members:
:undoc-members:
:show-inheritance:
GPy.mappings.kernel module GPy.mappings.kernel module
-------------------------- --------------------------
@ -28,6 +36,14 @@ GPy.mappings.mlp module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.mappings.symbolic module
----------------------------
.. automodule:: GPy.mappings.symbolic
:members:
:undoc-members:
:show-inheritance:
Module contents Module contents
--------------- ---------------

64
doc/GPy.models.rst
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@ -20,14 +20,6 @@ GPy.models.bcgplvm module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.fitc_classification module
-------------------------------------
.. automodule:: GPy.models.fitc_classification
:members:
:undoc-members:
:show-inheritance:
GPy.models.gp_classification module GPy.models.gp_classification module
----------------------------------- -----------------------------------
@ -36,6 +28,30 @@ GPy.models.gp_classification module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.gp_coregionalized_regression module
----------------------------------------------
.. automodule:: GPy.models.gp_coregionalized_regression
:members:
:undoc-members:
:show-inheritance:
GPy.models.gp_heteroscedastic_regression module
-----------------------------------------------
.. automodule:: GPy.models.gp_heteroscedastic_regression
:members:
:undoc-members:
:show-inheritance:
GPy.models.gp_kronecker_gaussian_regression module
--------------------------------------------------
.. automodule:: GPy.models.gp_kronecker_gaussian_regression
:members:
:undoc-members:
:show-inheritance:
GPy.models.gp_multioutput_regression module GPy.models.gp_multioutput_regression module
------------------------------------------- -------------------------------------------
@ -52,6 +68,14 @@ GPy.models.gp_regression module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.gp_var_gauss module
------------------------------
.. automodule:: GPy.models.gp_var_gauss
:members:
:undoc-members:
:show-inheritance:
GPy.models.gplvm module GPy.models.gplvm module
----------------------- -----------------------
@ -84,6 +108,14 @@ GPy.models.sparse_gp_classification module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.sparse_gp_coregionalized_regression module
-----------------------------------------------------
.. automodule:: GPy.models.sparse_gp_coregionalized_regression
:members:
:undoc-members:
:show-inheritance:
GPy.models.sparse_gp_multioutput_regression module GPy.models.sparse_gp_multioutput_regression module
-------------------------------------------------- --------------------------------------------------
@ -108,6 +140,22 @@ GPy.models.sparse_gplvm module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.ss_gplvm module
--------------------------
.. automodule:: GPy.models.ss_gplvm
:members:
:undoc-members:
:show-inheritance:
GPy.models.ss_mrd module
------------------------
.. automodule:: GPy.models.ss_mrd
:members:
:undoc-members:
:show-inheritance:
GPy.models.svigp_regression module GPy.models.svigp_regression module
---------------------------------- ----------------------------------

30
doc/GPy.plotting.matplot_dep.latent_space_visualizations.controllers.rst Normal file
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GPy.plotting.matplot_dep.latent_space_visualizations.controllers package
========================================================================
Submodules
----------
GPy.plotting.matplot_dep.latent_space_visualizations.controllers.axis_event_controller module
---------------------------------------------------------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations.controllers.axis_event_controller
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.latent_space_visualizations.controllers.imshow_controller module
-----------------------------------------------------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations.controllers.imshow_controller
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations.controllers
:members:
:undoc-members:
:show-inheritance:

17
doc/GPy.plotting.matplot_dep.latent_space_visualizations.rst Normal file
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GPy.plotting.matplot_dep.latent_space_visualizations package
============================================================
Subpackages
-----------
.. toctree::
GPy.plotting.matplot_dep.latent_space_visualizations.controllers
Module contents
---------------
.. automodule:: GPy.plotting.matplot_dep.latent_space_visualizations
:members:
:undoc-members:
:show-inheritance:

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GPy.plotting.matplot_dep package
================================
Subpackages
-----------
.. toctree::
GPy.plotting.matplot_dep.latent_space_visualizations
Submodules
----------
GPy.plotting.matplot_dep.Tango module
-------------------------------------
.. automodule:: GPy.plotting.matplot_dep.Tango
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.base_plots module
------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.base_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.dim_reduction_plots module
---------------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.dim_reduction_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.img_plots module
-----------------------------------------
.. automodule:: GPy.plotting.matplot_dep.img_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.inference_plots module
-----------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.inference_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.kernel_plots module
--------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.kernel_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.mapping_plots module
---------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.mapping_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.maps module
------------------------------------
.. automodule:: GPy.plotting.matplot_dep.maps
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.models_plots module
--------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.models_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.netpbmfile module
------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.netpbmfile
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.priors_plots module
--------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.priors_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.ssgplvm module
---------------------------------------
.. automodule:: GPy.plotting.matplot_dep.ssgplvm
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.svig_plots module
------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.svig_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.variational_plots module
-------------------------------------------------
.. automodule:: GPy.plotting.matplot_dep.variational_plots
:members:
:undoc-members:
:show-inheritance:
GPy.plotting.matplot_dep.visualize module
-----------------------------------------
.. automodule:: GPy.plotting.matplot_dep.visualize
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.plotting.matplot_dep
:members:
:undoc-members:
:show-inheritance:

17
doc/GPy.plotting.rst Normal file
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@ -0,0 +1,17 @@
GPy.plotting package
====================
Subpackages
-----------
.. toctree::
GPy.plotting.matplot_dep
Module contents
---------------
.. automodule:: GPy.plotting
:members:
:undoc-members:
:show-inheritance:

1
doc/GPy.rst
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@ -13,6 +13,7 @@ Subpackages
GPy.likelihoods GPy.likelihoods
GPy.mappings GPy.mappings
GPy.models GPy.models
GPy.plotting
GPy.testing GPy.testing
GPy.util GPy.util

98
doc/GPy.testing.rst
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@ -4,22 +4,6 @@ GPy.testing package
Submodules Submodules
---------- ----------
GPy.testing.bgplvm_tests module
-------------------------------
.. automodule:: GPy.testing.bgplvm_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.cgd_tests module
----------------------------
.. automodule:: GPy.testing.cgd_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.examples_tests module GPy.testing.examples_tests module
--------------------------------- ---------------------------------
@ -28,10 +12,18 @@ GPy.testing.examples_tests module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.testing.gplvm_tests module GPy.testing.fitc module
------------------------------ -----------------------
.. automodule:: GPy.testing.gplvm_tests .. automodule:: GPy.testing.fitc
:members:
:undoc-members:
:show-inheritance:
GPy.testing.index_operations_tests module
-----------------------------------------
.. automodule:: GPy.testing.index_operations_tests
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
@ -44,18 +36,42 @@ GPy.testing.kernel_tests module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.testing.mapping_tests module GPy.testing.likelihood_tests module
-------------------------------- -----------------------------------
.. automodule:: GPy.testing.mapping_tests .. automodule:: GPy.testing.likelihood_tests
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.testing.mrd_tests module GPy.testing.model_tests module
---------------------------- ------------------------------
.. automodule:: GPy.testing.mrd_tests .. automodule:: GPy.testing.model_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.observable_tests module
-----------------------------------
.. automodule:: GPy.testing.observable_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.parameterized_tests module
--------------------------------------
.. automodule:: GPy.testing.parameterized_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.pickle_tests module
-------------------------------
.. automodule:: GPy.testing.pickle_tests
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
@ -68,38 +84,6 @@ GPy.testing.prior_tests module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.testing.psi_stat_expectation_tests module
---------------------------------------------
.. automodule:: GPy.testing.psi_stat_expectation_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.psi_stat_gradient_tests module
------------------------------------------
.. automodule:: GPy.testing.psi_stat_gradient_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.sparse_gplvm_tests module
-------------------------------------
.. automodule:: GPy.testing.sparse_gplvm_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.unit_tests module
-----------------------------
.. automodule:: GPy.testing.unit_tests
:members:
:undoc-members:
:show-inheritance:
Module contents Module contents
--------------- ---------------

149
doc/GPy.util.rst
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@ -1,20 +1,21 @@
GPy.util package GPy.util package
================ ================
Subpackages
-----------
.. toctree::
GPy.util.latent_space_visualizations
Submodules Submodules
---------- ----------
GPy.util.Tango module GPy.util.block_matrices module
--------------------- ------------------------------
.. automodule:: GPy.util.Tango .. automodule:: GPy.util.block_matrices
:members:
:undoc-members:
:show-inheritance:
GPy.util.caching module
-----------------------
.. automodule:: GPy.util.caching
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
@ -27,6 +28,14 @@ GPy.util.classification module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.config module
----------------------
.. automodule:: GPy.util.config
:members:
:undoc-members:
:show-inheritance:
GPy.util.datasets module GPy.util.datasets module
------------------------ ------------------------
@ -35,6 +44,14 @@ GPy.util.datasets module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.debug module
---------------------
.. automodule:: GPy.util.debug
:members:
:undoc-members:
:show-inheritance:
GPy.util.decorators module GPy.util.decorators module
-------------------------- --------------------------
@ -43,6 +60,46 @@ GPy.util.decorators module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.diag module
--------------------
.. automodule:: GPy.util.diag
:members:
:undoc-members:
:show-inheritance:
GPy.util.erfcx module
---------------------
.. automodule:: GPy.util.erfcx
:members:
:undoc-members:
:show-inheritance:
GPy.util.functions module
-------------------------
.. automodule:: GPy.util.functions
:members:
:undoc-members:
:show-inheritance:
GPy.util.gpu_init module
------------------------
.. automodule:: GPy.util.gpu_init
:members:
:undoc-members:
:show-inheritance:
GPy.util.initialization module
------------------------------
.. automodule:: GPy.util.initialization
:members:
:undoc-members:
:show-inheritance:
GPy.util.linalg module GPy.util.linalg module
---------------------- ----------------------
@ -51,6 +108,22 @@ GPy.util.linalg module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.linalg_gpu module
--------------------------
.. automodule:: GPy.util.linalg_gpu
:members:
:undoc-members:
:show-inheritance:
GPy.util.ln_diff_erfs module
----------------------------
.. automodule:: GPy.util.ln_diff_erfs
:members:
:undoc-members:
:show-inheritance:
GPy.util.misc module GPy.util.misc module
-------------------- --------------------
@ -67,6 +140,14 @@ GPy.util.mocap module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.mpi module
-------------------
.. automodule:: GPy.util.mpi
:members:
:undoc-members:
:show-inheritance:
GPy.util.multioutput module GPy.util.multioutput module
--------------------------- ---------------------------
@ -75,18 +156,34 @@ GPy.util.multioutput module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.plot module GPy.util.netpbmfile module
-------------------- --------------------------
.. automodule:: GPy.util.plot .. automodule:: GPy.util.netpbmfile
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.plot_latent module GPy.util.normalizer module
--------------------------- --------------------------
.. automodule:: GPy.util.plot_latent .. automodule:: GPy.util.normalizer
:members:
:undoc-members:
:show-inheritance:
GPy.util.parallel module
------------------------
.. automodule:: GPy.util.parallel
:members:
:undoc-members:
:show-inheritance:
GPy.util.pca module
-------------------
.. automodule:: GPy.util.pca
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
@ -99,18 +196,26 @@ GPy.util.squashers module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.univariate_Gaussian module GPy.util.subarray_and_sorting module
----------------------------------- ------------------------------------
.. automodule:: GPy.util.univariate_Gaussian .. automodule:: GPy.util.subarray_and_sorting
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.util.visualize module GPy.util.symbolic module
------------------------- ------------------------
.. automodule:: GPy.util.visualize .. automodule:: GPy.util.symbolic
:members:
:undoc-members:
:show-inheritance:
GPy.util.univariate_Gaussian module
-----------------------------------
.. automodule:: GPy.util.univariate_Gaussian
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:

5
doc/tuto_creating_new_models.rst
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@ -39,8 +39,9 @@ Obligatory methods
:py:meth:`~GPy.core.model.Model.parameters_changed` : :py:meth:`~GPy.core.model.Model.parameters_changed` :
Updates the internal state of the model and sets the gradient of Updates the internal state of the model and sets the gradient of
each parameter handle in the hierarchy with respect to the each parameter handle in the hierarchy with respect to the
log_likelihod. Thus here we need to put the negative derivative of log_likelihod. Thus here we need to set the negative derivative of
the rosenbrock function: the rosenbrock function for the parameters. In this case it is the
gradient for self.X:
self.X.gradient = -scipy.optimize.rosen_der(self.X) self.X.gradient = -scipy.optimize.rosen_der(self.X)

31
doc/tuto_interacting_with_models.rst
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@ -40,24 +40,21 @@ is shown. For each parameter, the table contains the name
of the parameter, the current value, and in case there are of the parameter, the current value, and in case there are
defined: constraints, ties and prior distrbutions associated. :: defined: constraints, ties and prior distrbutions associated. ::
Log-likelihood: 6.309e+02 Name : sparse gp
Log-likelihood : -405.646051581
Number of Parameters : 8
Parameters:
sparse_gp. | Value | Constraint | Prior | Tied to
inducing inputs | (5, 1) | | |
rbf.variance | 1.0 | +ve | |
rbf.lengthscale | 1.0 | +ve | |
Gaussian_noise.variance | 1.0 | +ve | |
Name | Value | Constraints | Ties | Prior In this case the kernel parameters (``rbf.variance``,
------------------------------------------------------------------ ``rbf.lengthscale``) as well as
iip_0_0 | -1.4671 | | | the likelihood noise parameter (``Gaussian_noise.variance``), are constrained
iip_1_0 | 2.6378 | | | to be positive, while the inducing inputs have no
iip_2_0 | -0.0396 | | |
iip_3_0 | -2.6372 | | |
iip_4_0 | 1.4704 | | |
rbf_variance | 1.5672 | (+ve) | |
rbf_lengthscale | 2.5625 | (+ve) | |
white_variance | 0.0000 | (+ve) | |
noise_variance | 0.0022 | (+ve) | |
In this case the kernel parameters (``rbf_variance``,
``rbf_lengthscale`` and ``white_variance``) as well as
the noise parameter (``noise_variance``), are constrained
to be positive, while the inducing inputs have not
constraints associated. Also there are no ties or prior defined. constraints associated. Also there are no ties or prior defined.
Setting and fetching parameters by name Setting and fetching parameters by name