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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:

61
doc/GPy.core.rst
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GPy.core package
================
Subpackages
-----------
.. toctree::
GPy.core.parameterization
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
------------------
@ -28,14 +19,6 @@ GPy.core.gp module
:undoc-members:
:show-inheritance:
GPy.core.gp_base module
-----------------------
.. automodule:: GPy.core.gp_base
:members:
:undoc-members:
:show-inheritance:
GPy.core.mapping module
-----------------------
@ -52,22 +35,6 @@ GPy.core.model module
:undoc-members:
: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
-------------------------
@ -76,6 +43,14 @@ GPy.core.sparse_gp module
:undoc-members:
:show-inheritance:
GPy.core.sparse_gp_mpi module
-----------------------------
.. automodule:: GPy.core.sparse_gp_mpi
:members:
:undoc-members:
:show-inheritance:
GPy.core.svigp module
---------------------
@ -84,10 +59,10 @@ GPy.core.svigp module
:undoc-members:
:show-inheritance:
GPy.core.transformations module
-------------------------------
GPy.core.symbolic module
------------------------
.. automodule:: GPy.core.transformations
.. automodule:: GPy.core.symbolic
:members:
:undoc-members:
:show-inheritance:

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

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doc/GPy.inference.latent_function_inference.rst Normal file
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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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doc/GPy.inference.optimization.rst Normal file
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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
=====================
Submodules
----------
Subpackages
-----------
GPy.inference.conjugate_gradient_descent module
-----------------------------------------------
.. 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:
.. toctree::
GPy.inference.latent_function_inference
GPy.inference.optimization
Module contents
---------------

27
doc/GPy.kern.rst
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@ -1,33 +1,6 @@
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
---------------

113
doc/GPy.likelihoods.rst
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@ -1,28 +1,29 @@
GPy.likelihoods package
=======================
Subpackages
-----------
.. toctree::
GPy.likelihoods.noise_models
Submodules
----------
GPy.likelihoods.ep module
-------------------------
GPy.likelihoods.bernoulli module
--------------------------------
.. automodule:: GPy.likelihoods.ep
.. automodule:: GPy.likelihoods.bernoulli
:members:
:undoc-members:
: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:
:undoc-members:
:show-inheritance:
@ -35,14 +36,6 @@ GPy.likelihoods.gaussian module
:undoc-members:
:show-inheritance:
GPy.likelihoods.gaussian_mixed_noise module
-------------------------------------------
.. automodule:: GPy.likelihoods.gaussian_mixed_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.likelihood module
---------------------------------
@ -51,10 +44,82 @@ GPy.likelihoods.likelihood module
:undoc-members:
: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:
:undoc-members:
:show-inheritance:

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

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

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:

141
doc/GPy.plotting.matplot_dep.rst Normal file
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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.mappings
GPy.models
GPy.plotting
GPy.testing
GPy.util

98
doc/GPy.testing.rst
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@ -4,22 +4,6 @@ GPy.testing package
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
---------------------------------
@ -28,10 +12,18 @@ GPy.testing.examples_tests module
:undoc-members:
: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:
:undoc-members:
:show-inheritance:
@ -44,18 +36,42 @@ GPy.testing.kernel_tests module
:undoc-members:
:show-inheritance:
GPy.testing.mapping_tests module
--------------------------------
GPy.testing.likelihood_tests module
-----------------------------------
.. automodule:: GPy.testing.mapping_tests
.. automodule:: GPy.testing.likelihood_tests
:members:
:undoc-members:
: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:
:undoc-members:
:show-inheritance:
@ -68,38 +84,6 @@ GPy.testing.prior_tests module
:undoc-members:
: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
---------------

149
doc/GPy.util.rst
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@ -1,20 +1,21 @@
GPy.util package
================
Subpackages
-----------
.. toctree::
GPy.util.latent_space_visualizations
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:
:undoc-members:
:show-inheritance:
@ -27,6 +28,14 @@ GPy.util.classification module
:undoc-members:
:show-inheritance:
GPy.util.config module
----------------------
.. automodule:: GPy.util.config
:members:
:undoc-members:
:show-inheritance:
GPy.util.datasets module
------------------------
@ -35,6 +44,14 @@ GPy.util.datasets module
:undoc-members:
:show-inheritance:
GPy.util.debug module
---------------------
.. automodule:: GPy.util.debug
:members:
:undoc-members:
:show-inheritance:
GPy.util.decorators module
--------------------------
@ -43,6 +60,46 @@ GPy.util.decorators module
:undoc-members:
: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
----------------------
@ -51,6 +108,22 @@ GPy.util.linalg module
:undoc-members:
: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
--------------------
@ -67,6 +140,14 @@ GPy.util.mocap module
:undoc-members:
:show-inheritance:
GPy.util.mpi module
-------------------
.. automodule:: GPy.util.mpi
:members:
:undoc-members:
:show-inheritance:
GPy.util.multioutput module
---------------------------
@ -75,18 +156,34 @@ GPy.util.multioutput module
:undoc-members:
:show-inheritance:
GPy.util.plot module
--------------------
GPy.util.netpbmfile module
--------------------------
.. automodule:: GPy.util.plot
.. automodule:: GPy.util.netpbmfile
:members:
:undoc-members:
: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:
:undoc-members:
:show-inheritance:
@ -99,18 +196,26 @@ GPy.util.squashers module
:undoc-members:
: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:
:undoc-members:
: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:
:undoc-members:
: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` :
Updates the internal state of the model and sets the gradient of
each parameter handle in the hierarchy with respect to the
log_likelihod. Thus here we need to put the negative derivative of
the rosenbrock function:
log_likelihod. Thus here we need to set the negative derivative of
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)

31
doc/tuto_interacting_with_models.rst
View file

@ -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
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
------------------------------------------------------------------
iip_0_0 | -1.4671 | | |
iip_1_0 | 2.6378 | | |
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
In this case the kernel parameters (``rbf.variance``,
``rbf.lengthscale``) as well as
the likelihood noise parameter (``Gaussian_noise.variance``), are constrained
to be positive, while the inducing inputs have no
constraints associated. Also there are no ties or prior defined.
Setting and fetching parameters by name