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index 66a36c0b4e92510b9451d96e2388f2b653874d58..cd0a90191d6da306e4ed78ddc928e4489d4761a6 100644
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--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_inference.BayesInference.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_inference.BayesInference.html
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<link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
- <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../beam.html">Beam</a></li>
<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
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<li class="toctree-l1 current has-children"><a class="reference internal" href="../api.html">API</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" role="switch" type="checkbox"/><label for="toctree-checkbox-3"><div class="visually-hidden">Toggle navigation of API</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_inference.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_inference.html
index 2e6a799c66b9595083e82a705e8be70449c53eca..1fa6677318b8af94fc93ac68353acfb3ccdebfed 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_inference.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_inference.html
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- <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../beam.html">Beam</a></li>
<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
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</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
-</li>
<li class="toctree-l1 current has-children"><a class="reference internal" href="../api.html">API</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" role="switch" type="checkbox"/><label for="toctree-checkbox-3"><div class="visually-hidden">Toggle navigation of API</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.BayesModelComparison.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.BayesModelComparison.html
index a642297898b9436e37aa8c5587d79eadf6645d12..37db0dba49b9ccf95ea6dc938ad174f9ffbded54 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.BayesModelComparison.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.BayesModelComparison.html
@@ -10,7 +10,7 @@
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- <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../beam.html">Beam</a></li>
<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
-</li>
<li class="toctree-l1 current has-children"><a class="reference internal" href="../api.html">API</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" role="switch" type="checkbox"/><label for="toctree-checkbox-3"><div class="visually-hidden">Toggle navigation of API</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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- <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
</body>
</html>
\ No newline at end of file
diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.html
index 09a6f0253b9ae2bfe837416ef2bd36b31e3e73ad..d2ab1583f9e6d5c96e3ca3ebf6e643394374121f 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.bayes_model_comparison.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
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- <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../beam.html">Beam</a></li>
<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.Discrepancy.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.Discrepancy.html
index 63d0d4923acc7b9c361310abc271d4c902b7350e..79f36c04fb3178d0b41b6af61e002a94dcf08282 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.Discrepancy.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.Discrepancy.html
@@ -10,7 +10,7 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.html
index 42e560e0cdd72b353bd4841f03776ff24fa0c3d1..dbded702238ab5044ef67d43f65697212115692d 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.discrepancy.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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index 8e482570c67b8e42a307711c13c5ea2e57713022..7f936229549e4d0d37d5946401a70921e408f350 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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@@ -408,6 +408,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.MCMC.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.MCMC.html
index 6833c641e34ba9c95215841a557a531b8c225bd3..bb9aba4867fd641cd202d1a09896ee91e935398d 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.MCMC.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.MCMC.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.gelman_rubin.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.gelman_rubin.html
index 0021117122fe2976c9f2c7c2a47526618355ad70..2dd7b60ddc2d68041d4fc6369011f3658074653d 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.gelman_rubin.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.gelman_rubin.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.html b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.html
index 5adef4ccd674b5aa39980b760ab14a735e1d08a0..3906931dc8849acc3fb755883e5031d39928212d 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.bayes_inference.mcmc.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
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-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.html b/docs/build/html/_autosummary/bayesvalidrox.html
index 095b40c43274644968229360c3b437a31f2dba92..8148bd67bfcb5b13afcb66ec7eee5e3ea7ddd50c 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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-</li>
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@@ -408,6 +408,6 @@
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+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
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\ No newline at end of file
diff --git a/docs/build/html/_autosummary/bayesvalidrox.post_processing.html b/docs/build/html/_autosummary/bayesvalidrox.post_processing.html
index c1951eed0991f4cabf67bceac175da895e9caa85..a30f0900936708d96732f84fed022cf5f16250d4 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.post_processing.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.post_processing.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
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</ul>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.PostProcessing.html b/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.PostProcessing.html
index fe64cb485f99d69e0a5946081bd4089113b08990..23bc022a5c750b43f38ccbb9768dffc1108740e5 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.PostProcessing.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.PostProcessing.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.html b/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.html
index 470ca28f37aeb05b37c623755877cae3d64a95be..752be7e7b4556b87c2f5f1f455d399a40c939bc4 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.post_processing.post_processing.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.pylink.html b/docs/build/html/_autosummary/bayesvalidrox.pylink.html
index 264d58b268f9d2e31d68f55d31fb4e3b87fda2e6..a92f4eadd04edff924bd7549ff14d2ee09b696d2 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.pylink.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.pylink.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
</ul>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.PyLinkForwardModel.html b/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.PyLinkForwardModel.html
index 404a599539379da6cf37ec9bd7e273327cbcecd3..3fd01d6459741ff9780d56c32c7d6589b42fdb9a 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.PyLinkForwardModel.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.PyLinkForwardModel.html
@@ -10,7 +10,7 @@
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- <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.html b/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.html
index 555330a8bc61295248e599bb02c9701b6d0dd056..e3ae83058146d5bc708957012e6cc9f14f78ce35 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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index fe0fec69e578c1304abe292bccfaa432adf3a680..dede4fc9a6c87dde775b8e12c89e0af8c2037893 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.within_range.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.pylink.pylink.within_range.html
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.adaptPlot.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.adaptPlot.html
index 99936d5417dd657825265134467791527be67813..f2c59c45bddc8695b07609fed2ada06f79053fff 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.adaptPlot.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.adaptPlot.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.html
index a63e69ad7af99e6d10c71a3c3644dcb47f64f51f..208623027e688f37bd944c064fbbdb309393864f 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.adaptPlot.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.apoly_construction.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.apoly_construction.html
index 7c8ecb72a88b70267684995470c7aba188f8476b..44563edabcfe5d9bf06900bf69fa7bd38d85c866 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.apoly_construction.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.apoly_construction.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.html
index 6e6c6281755eaf87874e54ee6c1e75a00fd7538e..0841b4ece045228c72b96369727f8bcc4651659a 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.apoly_construction.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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index 1cb003d7de5c2f1a8b733b931d1bcd979ee21ed7..cad9e1c779c38955764be5f15a8254733e93aaec 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.BayesianLinearRegression.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.BayesianLinearRegression.html
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.EBLinearRegression.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.EBLinearRegression.html
index 486294e045cebdcf2be190e2219311d65ac3610b..78b455a0737ee544faf7d8b93a17d2c06fe9c583 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.EBLinearRegression.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.EBLinearRegression.html
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@@ -164,8 +164,14 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.VBLinearRegression.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.VBLinearRegression.html
index 01eff226dc0f4be40f70c049e8d02ee3ae85ad0e..1851096825123bf090eba7743c2b84c727344b89 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.VBLinearRegression.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.VBLinearRegression.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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+</li>
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@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
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@@ -776,6 +776,6 @@ sub-estimator of a meta-estimator, e.g. used inside a
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+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
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\ No newline at end of file
diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.gamma_mean.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.gamma_mean.html
index 4f599790141bb6ef4f6788290a285576357e1902..044b88f8e5f1fd3b95ab4618eb9cfbed93e62841 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.gamma_mean.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.gamma_mean.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.html
index 25c6663efd4c012548b01e34dc2c4725e5331b7d..0033214ac3809c3e22ec42832b5149bf46dfc279 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.bayes_linear.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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@@ -433,6 +433,6 @@
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+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html
index d6f4907b736b20b925592151125396c44de62a21..dbacf659767718cedf1786f96f0cdb944e0cf68a 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html
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@@ -164,8 +164,16 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../model_description.html">Models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../al_description.html">Active learning: iteratively expanding the training set</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +183,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.hellinger_distance.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.hellinger_distance.html
index e2daf1a9dd7a873703ea0196d9b9e9e1d7f65b11..ffe7c62a38e0ec03fa1730b6ab609e69f0d1e79a 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.hellinger_distance.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.hellinger_distance.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,16 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../model_description.html">Models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../al_description.html">Active learning: iteratively expanding the training set</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +183,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.html
index 3e7323ed619d86a088f1d8be9541a965bf400309..01ccaf1be539dfa67bf420fe9db2d963c99ba8ad 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,16 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../model_description.html">Models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../al_description.html">Active learning: iteratively expanding the training set</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +183,6 @@
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index cf4674919feb4585169d3238db5491d4f89b53ed..90150becd7bc8a8bba271b4f8c91c06ad5c71c0d 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.logpdf.html
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index a8b210d322270317dfac5fe74a189b4ba9eca122..573e622e093d9e63ddb69e0906954e3195a1ca4b 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.engine.subdomain.html
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index 9e8e90cfa6b7d729e2269c9a289825e489bd4ddb..80f24a101786c43481925f5b39c17ad1566e460f 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.eval_rec_rule.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.eval_rec_rule.html
@@ -10,7 +10,7 @@
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+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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index 6ed2f6d0fb8873df72f016b971b914fe2dd7c625..e5be4529198e7c1925bd24927dbc29714676f28e 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.eval_rec_rule_arbitrary.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.eval_rec_rule_arbitrary.html
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@@ -175,12 +181,6 @@
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index 0092cf5276a5af49f773ba538c4491541dc6f1a2..b704f3d3ed736962f670bd828f95a101873f096e 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.eval_univ_basis.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.eval_univ_basis.html
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index d51f32797a3204e47a7c26e2ae9bac48cba357f2..152ac0cc69ec773c28e708006de76d8a3d5e5731 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.html
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index dfd5f5911f92607f01e0b56a0bcf7183dd0eaf76..11c59eb6803d666fa37798d59e0cfb5890c63348 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.poly_rec_coeffs.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.poly_rec_coeffs.html
@@ -10,7 +10,7 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.Exploration.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.Exploration.html
index 2e002e43855de7ac7755585f2adbf8ad667f72cf..cd723f3ffb0336cfde96ee808f77b8215c75518e 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.Exploration.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.Exploration.html
@@ -10,7 +10,7 @@
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.html
index 352ff3b93d6f81f065738ef6efffbce1c77ae5b8..e1ac08e7f9c7bcbfe7cb8e00c036b85b02bbc647 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.exploration.html
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index 1287f3d4381b9becd8e42192bf30c433aff1ebb9..c03a28785096bff0540ef5b6484f856f1ec11868 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.cross_truncate.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.cross_truncate.html
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -448,6 +448,6 @@ truncation criteria holds.</p>
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+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
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\ No newline at end of file
diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.glexindex.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.glexindex.html
index 5b23211590e1076ec31c7eb56e3413ff25c93247..c539a49fc5f6ff8d81d886a2b324ad58e05b4359 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.glexindex.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.glexindex.html
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.html
index 61a05b4c46479cc1abe591698dc90dcb74d7e323..23c6ccaf9b1c62ed712bb0a2518fa1a1bf154046 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.glexindex.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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@@ -405,6 +405,6 @@ Credit: Jonathan Feinberg
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+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.InputSpace.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.InputSpace.html
index 0ad981477750eb1466d2b0854aa50f0e326ef1ed..3267f5a5bcfeaf030c86c582e71ff2ceb886289f 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.InputSpace.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.InputSpace.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.html
index 5e042adc854b23b7607e191985a76a578c87a1fe..a6709b5e2bfd178a344872bdc2040762bda3e381 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.input_space.html
@@ -10,7 +10,7 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Input.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Input.html
index b5caa67c0a65d4ca57c9d5d302745cbbc45af3ba..b9176038b945603d3917133a8d6619b535d452a1 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Input.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Input.html
@@ -10,7 +10,7 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Marginal.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Marginal.html
index 7656938dc4434feac55976f4c90796b4d97be95a..76b367e00171da1f16dc39466870163311111c5c 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Marginal.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.Marginal.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.html
index a09b519051a800b2b47703d274dd44cad5ea76da..029c319cd8cb5349291475ca63bfe1c046b41b1d 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.inputs.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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index 6effdb4bede82af0ec0af886a5ddddcc25fbaac9..a779a0005a683cae0baf365641d5f7d8f335a6bc 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.OrthogonalMatchingPursuit.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.OrthogonalMatchingPursuit.html
@@ -10,7 +10,7 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.corr.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.corr.html
index 50503ba017693c5bfb791f76b7d0dcc0bc0ae79c..1786db353d68b904ebd8feb4ed5c1aef0baa68af 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.corr.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.corr.html
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@@ -175,12 +181,6 @@
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index 193d5a32019a6e61c0622c224914d68bacc34ec9..80f8889317e166a036ab6bb25931db0683fe574f 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.orthogonal_matching_pursuit.html
@@ -10,7 +10,7 @@
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.RegressionFastARD.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.RegressionFastARD.html
index 388c216b760afd06b146ea66f2ae1256bff57e94..416904a84e50b7320c99b2411370941863936a6f 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.RegressionFastARD.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.RegressionFastARD.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.html
index d158d469a459442cfb6cf8b4f93b8733d202fb6a..fd8ef6ea88ac3077dfb223e89be8b77e89aeeddd 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.html
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.update_precisions.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.update_precisions.html
index aa81538916c0ed6e547f084dffad6230d9a16e61..a56113eb822068c738c5395254282274a10f99e2 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.update_precisions.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.update_precisions.html
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@@ -164,8 +164,14 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.RegressionFastLaplace.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.RegressionFastLaplace.html
index 55ab1b8fab026ea76f690c2bc0045876664f2b85..ec46718c4c960aa78bc09bfb81be20bccb12e5de 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.RegressionFastLaplace.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.RegressionFastLaplace.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.html
index 7f57932c04ec08a7c10b4ba78bba514b2273f5e0..57bdb940db768c2ea82143869752f165c38690f6 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html
index 06325c8d79515ed4198beff7f8fbf41c0d4ff983..9f4ce9efa7114ac11c39ebdcad45521f09bc7e37 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.corr_loocv_error.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.corr_loocv_error.html
index a7be435bfa2cfe79fefec92084fbdc23133741f4..ea62a231fa4d5ce2bb0190d26cf223d2e0e149ef 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.corr_loocv_error.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.corr_loocv_error.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
</form>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.create_psi.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.create_psi.html
index ea19bdf2341ea2dee56f76e9c2469de7e581f2ee..290dd7f7294dd2d94aebf4979abd8e60da4224e7 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.create_psi.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.create_psi.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.gaussian_process_emulator.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.gaussian_process_emulator.html
index ef192202b72cf0c9bfab4e46effc98622155d6c3..b548770840d1b4158226ea58047cacf8ea2f1815 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.gaussian_process_emulator.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.gaussian_process_emulator.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="../borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="../pollution.html">Pollution</a></li>
</ul>
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diff --git a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.html b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.html
index c5321b4dae6b08ce4587e3b75d6042b64be8d468..22ed21b9a2b9521c73f8f4075713be3b2936f1a5 100644
--- a/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.html
+++ b/docs/build/html/_autosummary/bayesvalidrox.surrogate_models.surrogate_models.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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+<li class="toctree-l1 has-children"><a class="reference internal" href="../examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
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-<li class="toctree-l2"><a class="reference internal" href="../input_description.html">Priors, input space and experimental design</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
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diff --git a/docs/build/html/_sources/al_description.rst.txt b/docs/build/html/_sources/al_description.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..636fa7877bb9b02fd4512c11459647e3c9a57ef7
--- /dev/null
+++ b/docs/build/html/_sources/al_description.rst.txt
@@ -0,0 +1,8 @@
+Active learning: iteratively expanding the training set
+*******************************************************
+
+
+
+.. image:: ../diagrams/active_learning_reduced.png
+ :width: 550
+ :alt: UML diagram for the classes and functions used in active learning in BayesValidRox.
\ No newline at end of file
diff --git a/docs/build/html/_sources/al_training.rst.txt b/docs/build/html/_sources/al_training.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5a68dc7f90b2c116440c02f711ba46490b9b0bd
--- /dev/null
+++ b/docs/build/html/_sources/al_training.rst.txt
@@ -0,0 +1,2 @@
+Active learning: iteratively expanding the training set
+*******************************************************
\ No newline at end of file
diff --git a/docs/build/html/_sources/bayes_description.rst.txt b/docs/build/html/_sources/bayes_description.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cfd3a6a8c43868b09f404eafdd36594ed9c3c7d
--- /dev/null
+++ b/docs/build/html/_sources/bayes_description.rst.txt
@@ -0,0 +1,7 @@
+Bayesian inference and multi-model comparison
+*********************************************
+
+
+.. image:: ../diagrams/bayesian_validation.png
+ :width: 300
+ :alt: UML diagram for classes related to Bayesian inference and multi-model comparison.
diff --git a/docs/build/html/_sources/model_description.rst.txt b/docs/build/html/_sources/model_description.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f08ea0cd2ab6eb368f290d6121ce2e60fa1d35c8
--- /dev/null
+++ b/docs/build/html/_sources/model_description.rst.txt
@@ -0,0 +1,54 @@
+Models
+******
+
+.. container:: twocol
+
+ .. container:: leftside
+
+ BayesValidRox gives options to create interfaces for a variety of models with the class :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel`.
+
+ Its main function is to run the model on given samples and to read in and contain MC references and observations.
+
+ Models can be defined via python functions, shell commands or as general executables.
+ This allows for the use of BayesValidRox with a broad range of models and easy extension to models that are defined with e.g. UM-Bridge.
+
+ .. container:: rightside
+
+ .. image:: ../diagrams/model.png
+ :width: 150
+ :alt: UML diagram for the bayesvalidrox class :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel`.
+
+Example
+=======
+For this example we use a very simple model that maps the uncertain parameter :math:`X` from the example in :any:`input_description` to two outputs, the original value and its square.
+We define this model as a function ``model`` in a new file ``model.py``.
+This function takes a single realization of the uncertain parameter as a 2-dimensional ``np.array`` and returns a dictionary of model results.
+Here we use the key ``A`` for the sample values and ``B`` for their squares.
+Under the key ``x_values`` a list should be given that is of the same length as each output of the model for a single input.
+The values in this list can denote e.g. timesteps and are used in postprocessing as labels of the x-axis.
+
+>>> def model(sample):
+>>> square = sample*sample
+>>> outputs = {'A': sample, 'B': square, 'x_values': [0]}
+>>> return outputs
+
+In the main python file we can create an object of :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel` that links to this model.
+
+>>> from bayesvalidrox import PyLinkForwardModel
+
+We create an object of this class and set the ``link_type`` as 'Function' to indicate that this is a function in a python file.
+``py_file`` should be set to the filename of the model and ``name`` to the name of the function.
+Lastly we list the keys of the outputs that we are interested in.
+
+>>> Model = PyLinkForwardModel()
+>>> Model.link_type = 'Function'
+>>> Model.py_file = 'model'
+>>> Model.name = 'model'
+>>> Model.Output.names = ['A', 'B']
+
+With this we have completed an interface to our model.
+We can now evaluate this model on the samples created in the input example.
+
+>>> output, samples = Model.run_model_parallel(samples)
+
+Other types of model links can be found in :any:`examples`, e.g. :any:`beam` uses a shell command and parser.
diff --git a/docs/build/html/_sources/post_description.rst.txt b/docs/build/html/_sources/post_description.rst.txt
index 9950c8cf9ee8a3709506e18b2a68ec51a63f7fd4..af2172709f4581abfabdcfd06257edfa808aa501 100644
--- a/docs/build/html/_sources/post_description.rst.txt
+++ b/docs/build/html/_sources/post_description.rst.txt
@@ -1,2 +1,66 @@
-Postprocessing, Bayesian inference and Bayesian model comparison
-****************************************************************
\ No newline at end of file
+Postprocessing
+**************
+.. container:: twocol
+
+ .. container:: leftside
+
+ Postprocessing refers to evaluations and checks performed on a model to get an understanding of its properties and estimate its quality.
+ The BayesValidRox class :any:`bayesvalidrox.post_processing.post_processing.PostProcessing` includes functions that are applicable to all types of surrogate model.
+
+ * ``valid_metamodel``: visualizing some metamodel runs against the corresponding model runs
+ * ``check_accuracy``: computing the RMSE error of the surrogate model
+
+ .. container:: rightside
+
+ .. image:: ../diagrams/postprocessing.png
+ :width: 300
+ :alt: UML diagram for the classes and functions used in active learning in BayesValidRox.
+
+Postprocessing methods that are specific to a type of surrogate or training include
+
+* ``plot_moments``: visualizing the moments of a polynomial chaos expansion (PCE, aPCE)
+* ``sobol_indices``: calculating the Sobol' and Total Sobol' indices (PCE, aPCE)
+* ``plot_seq_design_diagnostics``: visualizing diagnostics that were evaluated during sequential training (surrogate trained with ``train_sequential``)
+
+
+Example
+=======
+We want to compare out trained surrogate from :any:`al_description` against its original model.
+
+>>> from bayesvalidrox import PostProcessing
+
+The postprocessing object expects the full engine. This allows it to perform both sampling, running the model and running the surrogate model.
+
+>>> PostProc = PostProcessing(Engine_)
+
+To gain an understanding of the approximation quality we use both ``valid_metamodel`` and ``check_accuracy``.
+
+>>> PostProc.valid_metamodel(n_samples=1)
+>>> PostProc.check_accuracy(n_samples=10)
+
+The visual comparison of model and metamodel results is saved in the folder ``Outputs_PostProcessing_calib``, while the accuracy check is given as console output.
+
+.. container:: twocol
+
+ .. container:: leftside
+
+ .. code-block:: py
+
+ >>>>> Errors of A <<<<<
+
+ Index | RMSE | Validation Error
+ -----------------------------------
+ 1 | 1.513e-07 | 2.224e-15
+
+ >>>>> Errors of B <<<<<
+
+ Index | RMSE | Validation Error
+ -----------------------------------
+ 1 | 5.045e-05 | 2.406e-11
+
+ .. container:: rightside
+
+ .. image:: ../../examples/user_guide/Outputs_PostProcessing_calib/Model_vs_PCEModel_y_1.pdf
+ :width: 400
+ :alt: Visual comparison of model and metamodel outputs
+
\ No newline at end of file
diff --git a/docs/build/html/_sources/surrogate_description.rst.txt b/docs/build/html/_sources/surrogate_description.rst.txt
index 676b73ba6599039c68c3b5c6830645f3e9793fb2..3b32fbe2eeea9fcdeb4d726d806bee68268c902f 100644
--- a/docs/build/html/_sources/surrogate_description.rst.txt
+++ b/docs/build/html/_sources/surrogate_description.rst.txt
@@ -1,2 +1,98 @@
Training surrogate models
-*************************
\ No newline at end of file
+*************************
+Surrogate models, also called metamodels, are models that are built on evaluations of full models with the goal to capture the full behaviour, but reduce the cost of evaluations.
+
+In BayesValidRox two types of surrogate model are available, polynomial chaos expansion and Gaussian processes.
+The Polynomial Chaos Expansion (PCE) and its variant the arbitrary Polynomial Chaos Expansion (aPC) build polynomials from the given distributions of uncertain inputs.
+Gaussian processes (GP) give kernel-based representations of the model results.
+
+The surrogate models are trained on datasets :math:`\mathcal{D}=(x_i, y_i)_{i=1,\dots,M)` that consist of :math:`M` samples of the uncertain parameters and the corresponding model outputs.
+We call this dataset the training data, with training samples :math:`(x_i)_{i=1,\dots,M)`.
+
+
+MetaModel and Engine classes
+============================
+BayesValidRox creates surrogate models as objects of the class :any:`bayesvalidrox.surrogate_models.surrogate_models.MetaModel`.
+Training is performed by the class :any:`bayesvalidrox.surrogate_models.engine.Engine`.
+
+.. image:: ../diagrams/metamod_training_reduced.png
+ :width: 800
+ :alt: UML diagram for metamodel-related classes in bayesvalidrox
+
+MetaModel options
+=================
+
+
+Training with the engine
+========================
+For training a surrogate model we use an object of class :any:`bayesvalidrox.surrogate_models.engine.Engine`.
+This needs to be given three things: the metamodel itself, the model that the metamodel should replace and the experimental design that matches the uncertain inputs for the model and metamodel.
+
+The standard method of training the surrogate is performed by the function ``train_normal()``.
+Other available training methods in BayesValidRox are presented in :any:`al_description`.
+
+For training the engine performs three main steps.
+
+1) Generating training samples from the experimental design.
+2) Evaluating the model on the training samples.
+3) Fitting the surrogate to the training dataset.
+
+Example
+=======
+We now build a surrogate model for the simple model from :any:`model_description` using the experimental design from :any:`input_description`.
+For this we need the classes :any:`bayesvalidrox.surrogate_models.surrogate_models.MetaModel` and :any:`bayesvalidrox.surrogate_models.engine.Engine`.
+
+>> from bayesvalidrox import MetaModel, Engine
+
+First we set up the surrogate model and tell it to consider the uncertain parameters defined in ``Inputs`` as its input parameters.
+
+>>> MetaMod = MetaModel(Inputs)
+
+Then we specify what type of surrogate we want and its properties.
+Here we use an aPCE with maximal polynomial degree 3 and want to use FastARD as the regression method.
+We set the value of the q-norm truncation scheme to 0.9.
+This combination will give us a sparse aPCE.
+
+>>> MetaMod.meta_model_type = 'aPCE'
+>>> MetaMod.pce_reg_method = 'FastARD'
+>>> MetaMod.pce_deg = 3
+>>> MetaMod.pce_q_norm = 0.85
+
+Before we start the actual training we need to set some training-related values for the experimental design.
+Most importantly we set the attribute ``method`` to 'normal' to indicate that no iterations are performed during the training and we set ``n_init_samples`` to our wanted number of training samples.
+
+.. warning::
+ The attribute ``method`` will be deprecated in further release.
+
+>>> ExpDesign.method = 'normal'
+>>> ExpDesign.n_init_samples = 10
+
+Like this the experimental design will generate 10 samples according to our previously set sampling method.
+Alternatively we can set the samples that we generated in :any:`input_description` as the training samples.
+For this the sampling method should be set to 'user' and our samples given as ``X``.
+
+>>> ExpDesign.sampling_method = 'user'
+>>> ExpDesign.root_samples = samples
+
+Now we create an engine object with the model, experimental design and surrogate model.
+With the function ``start_engine`` the engine performs its preparations for training.
+
+.. warning::
+ The function start_engine will likely be deprecated in future releases.
+
+>>> Engine_ = Engine(MetaMod, Model, ExpDesign)
+>>> Engine_.start_engine()
+
+Then we train the surrogate model.
+
+>>> Engine.train_normal()
+
+We can evaluate the trained surrogate model in two ways, via the engine, or directly.
+The evaluations return the mean approximation of the surrogate and its associated standard deviation.
+Evaluation via the surrogate model can make use of the sampling in the experimental design,
+
+>>> mean, stdev = Engine_.eval_metamodel(nsamples = 10)
+
+while for direct evaluation the exact set of samples has to be given.
+
+>>> mean, stdev = Engine_.MetaModel.eval_metamodel(samples)
diff --git a/docs/build/html/al_description.html b/docs/build/html/al_description.html
new file mode 100644
index 0000000000000000000000000000000000000000..8b449364dc0419d8c451d936443252aaae8eb0ee
--- /dev/null
+++ b/docs/build/html/al_description.html
@@ -0,0 +1,396 @@
+<!doctype html>
+<html class="no-js" lang="en" data-content_root="./">
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+
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+<li class="toctree-l2 current current-page"><a class="current reference internal" href="#">Active learning: iteratively expanding the training set</a></li>
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+<li class="toctree-l4 has-children"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.eval_rec_rule.html">bayesvalidrox.surrogate_models.eval_rec_rule</a><input class="toctree-checkbox" id="toctree-checkbox-19" name="toctree-checkbox-19" role="switch" type="checkbox"/><label for="toctree-checkbox-19"><div class="visually-hidden">Toggle navigation of bayesvalidrox.surrogate_models.eval_rec_rule</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+</ul>
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+<li class="toctree-l4 has-children"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.html">bayesvalidrox.surrogate_models.reg_fast_ard</a><input class="toctree-checkbox" id="toctree-checkbox-26" name="toctree-checkbox-26" role="switch" type="checkbox"/><label for="toctree-checkbox-26"><div class="visually-hidden">Toggle navigation of bayesvalidrox.surrogate_models.reg_fast_ard</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l5"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.reg_fast_ard.RegressionFastARD.html">bayesvalidrox.surrogate_models.reg_fast_ard.RegressionFastARD</a></li>
+</ul>
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+<li class="toctree-l4 has-children"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.html">bayesvalidrox.surrogate_models.reg_fast_laplace</a><input class="toctree-checkbox" id="toctree-checkbox-27" name="toctree-checkbox-27" role="switch" type="checkbox"/><label for="toctree-checkbox-27"><div class="visually-hidden">Toggle navigation of bayesvalidrox.surrogate_models.reg_fast_laplace</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+</ul>
+</li>
+<li class="toctree-l4 has-children"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.html">bayesvalidrox.surrogate_models.surrogate_models</a><input class="toctree-checkbox" id="toctree-checkbox-28" name="toctree-checkbox-28" role="switch" type="checkbox"/><label for="toctree-checkbox-28"><div class="visually-hidden">Toggle navigation of bayesvalidrox.surrogate_models.surrogate_models</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l5"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.create_psi.html">bayesvalidrox.surrogate_models.surrogate_models.create_psi</a></li>
+<li class="toctree-l5"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.gaussian_process_emulator.html">bayesvalidrox.surrogate_models.surrogate_models.gaussian_process_emulator</a></li>
+<li class="toctree-l5"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html">bayesvalidrox.surrogate_models.surrogate_models.MetaModel</a></li>
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+<h1>Active learning: iteratively expanding the training set<a class="headerlink" href="#active-learning-iteratively-expanding-the-training-set" title="Link to this heading">¶</a></h1>
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diff --git a/docs/build/html/analyticalfunction.html b/docs/build/html/analyticalfunction.html
index bc4fc92c60829f7b3f8d299a42154728ef7dca77..6e67d67ebc0a6b8222f47e680053d0023e13c191 100644
--- a/docs/build/html/analyticalfunction.html
+++ b/docs/build/html/analyticalfunction.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="_static/custom.css?v=3c2b257a" />
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</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
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+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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<li class="toctree-l2"><a class="reference internal" href="beam.html">Beam</a></li>
<li class="toctree-l2"><a class="reference internal" href="borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="pollution.html">Pollution</a></li>
</ul>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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diff --git a/docs/build/html/api.html b/docs/build/html/api.html
index c1d69b4778c3962ef59d30d2c010ef13d708b280..5658a734524e0c5ccf075ea438335743d9a1c9a8 100644
--- a/docs/build/html/api.html
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@@ -3,14 +3,14 @@
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+ <link rel="stylesheet" type="text/css" href="_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
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+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
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+<li class="toctree-l4 has-children"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.reg_fast_laplace.html">bayesvalidrox.surrogate_models.reg_fast_laplace</a><input class="toctree-checkbox" id="toctree-checkbox-27" name="toctree-checkbox-27" role="switch" type="checkbox"/><label for="toctree-checkbox-27"><div class="visually-hidden">Toggle navigation of bayesvalidrox.surrogate_models.reg_fast_laplace</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+</ul>
+</li>
+<li class="toctree-l4 has-children"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.html">bayesvalidrox.surrogate_models.surrogate_models</a><input class="toctree-checkbox" id="toctree-checkbox-28" name="toctree-checkbox-28" role="switch" type="checkbox"/><label for="toctree-checkbox-28"><div class="visually-hidden">Toggle navigation of bayesvalidrox.surrogate_models.surrogate_models</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l5"><a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.create_psi.html">bayesvalidrox.surrogate_models.surrogate_models.create_psi</a></li>
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diff --git a/docs/build/html/beam.html b/docs/build/html/beam.html
index bb607512cd198f46c7455194da4ea97ac56fcb65..1695c993287f0667381a7936b89150815c62e9f1 100644
--- a/docs/build/html/beam.html
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</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
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+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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@@ -175,12 +181,6 @@
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diff --git a/docs/build/html/borehole.html b/docs/build/html/borehole.html
index d7d4768575c6b01b3d37e6492c9d2a3deb70447d..818d19fe65554a33aa09819a9a7b574e7d480f96 100644
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+++ b/docs/build/html/borehole.html
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@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 current has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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@@ -175,12 +181,6 @@
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</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/examples.html b/docs/build/html/examples.html
index 10abc86c28771e880f127c4c43bfb92a79d918fc..4da7009a0497d5ec999b3a43ba2559d968f70a62 100644
--- a/docs/build/html/examples.html
+++ b/docs/build/html/examples.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
<link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
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- <link rel="stylesheet" type="text/css" href="_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 current has-children current-page"><a class="current reference internal" href="#">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 current has-children current-page"><a class="current reference internal" href="#">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
-</li>
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diff --git a/docs/build/html/ishigami.html b/docs/build/html/ishigami.html
index 6e9b23919b5375f1b77542fe87fd30bfa72ecad6..f9c499fe25d027c02d69a03fe3eb8bb868b2cb73 100644
--- a/docs/build/html/ishigami.html
+++ b/docs/build/html/ishigami.html
@@ -10,7 +10,7 @@
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
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- <link rel="stylesheet" type="text/css" href="_static/custom.css?v=da48c412" />
+ <link rel="stylesheet" type="text/css" href="_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 current has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
+<li class="toctree-l1 current has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
-</li>
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diff --git a/docs/build/html/model_description.html b/docs/build/html/model_description.html
new file mode 100644
index 0000000000000000000000000000000000000000..d7460501bc0c677cfaaaaba31cd5cfda45aa4507
--- /dev/null
+++ b/docs/build/html/model_description.html
@@ -0,0 +1,464 @@
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+ <i class="icon"><svg><use href="#svg-toc"></use></svg></i>
+ </label>
+ </div>
+ <article role="main">
+ <section id="models">
+<h1>Models<a class="headerlink" href="#models" title="Link to this heading">¶</a></h1>
+<div class="twocol docutils container">
+<div class="leftside docutils container">
+<p>BayesValidRox gives options to create interfaces for a variety of models with the class <a class="reference internal" href="_autosummary/bayesvalidrox.pylink.pylink.PyLinkForwardModel.html#bayesvalidrox.pylink.pylink.PyLinkForwardModel" title="bayesvalidrox.pylink.pylink.PyLinkForwardModel"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.pylink.pylink.PyLinkForwardModel</span></code></a>.</p>
+<blockquote>
+<div><p>Its main function is to run the model on given samples and to read in and contain MC references and observations.</p>
+<p>Models can be defined via python functions, shell commands or as general executables.
+This allows for the use of BayesValidRox with a broad range of models and easy extension to models that are defined with e.g. UM-Bridge.</p>
+</div></blockquote>
+</div>
+<div class="rightside docutils container">
+<a class="reference internal image-reference" href="_images/model.png"><img alt="UML diagram for the bayesvalidrox class :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel`." src="_images/model.png" style="width: 150px;" /></a>
+</div>
+</div>
+<section id="example">
+<h2>Example<a class="headerlink" href="#example" title="Link to this heading">¶</a></h2>
+<p>For this example we use a very simple model that maps the uncertain parameter <span class="math notranslate nohighlight">\(X\)</span> from the example in <a class="reference internal" href="input_description.html"><span class="doc">Priors, input space and experimental design</span></a> to two outputs, the original value and its square.
+We define this model as a function <code class="docutils literal notranslate"><span class="pre">model</span></code> in a new file <code class="docutils literal notranslate"><span class="pre">model.py</span></code>.
+This function takes a single realization of the uncertain parameter as a 2-dimensional <code class="docutils literal notranslate"><span class="pre">np.array</span></code> and returns a dictionary of model results.
+Here we use the key <code class="docutils literal notranslate"><span class="pre">A</span></code> for the sample values and <code class="docutils literal notranslate"><span class="pre">B</span></code> for their squares.
+Under the key <code class="docutils literal notranslate"><span class="pre">x_values</span></code> a list should be given that is of the same length as each output of the model for a single input.
+The values in this list can denote e.g. timesteps and are used in postprocessing as labels of the x-axis.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="k">def</span> <span class="nf">model</span><span class="p">(</span><span class="n">sample</span><span class="p">):</span>
+<span class="gp">>>> </span> <span class="n">square</span> <span class="o">=</span> <span class="n">sample</span><span class="o">*</span><span class="n">sample</span>
+<span class="gp">>>> </span> <span class="n">outputs</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'A'</span><span class="p">:</span> <span class="n">sample</span><span class="p">,</span> <span class="s1">'B'</span><span class="p">:</span> <span class="n">square</span><span class="p">,</span> <span class="s1">'x_values'</span><span class="p">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">]}</span>
+<span class="gp">>>> </span> <span class="k">return</span> <span class="n">outputs</span>
+</pre></div>
+</div>
+<p>In the main python file we can create an object of <a class="reference internal" href="_autosummary/bayesvalidrox.pylink.pylink.PyLinkForwardModel.html#bayesvalidrox.pylink.pylink.PyLinkForwardModel" title="bayesvalidrox.pylink.pylink.PyLinkForwardModel"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.pylink.pylink.PyLinkForwardModel</span></code></a> that links to this model.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">bayesvalidrox</span> <span class="kn">import</span> <span class="n">PyLinkForwardModel</span>
+</pre></div>
+</div>
+<p>We create an object of this class and set the <code class="docutils literal notranslate"><span class="pre">link_type</span></code> as ‘Function’ to indicate that this is a function in a python file.
+<code class="docutils literal notranslate"><span class="pre">py_file</span></code> should be set to the filename of the model and <code class="docutils literal notranslate"><span class="pre">name</span></code> to the name of the function.
+Lastly we list the keys of the outputs that we are interested in.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">Model</span> <span class="o">=</span> <span class="n">PyLinkForwardModel</span><span class="p">()</span>
+<span class="gp">>>> </span><span class="n">Model</span><span class="o">.</span><span class="n">link_type</span> <span class="o">=</span> <span class="s1">'Function'</span>
+<span class="gp">>>> </span><span class="n">Model</span><span class="o">.</span><span class="n">py_file</span> <span class="o">=</span> <span class="s1">'model'</span>
+<span class="gp">>>> </span><span class="n">Model</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s1">'model'</span>
+<span class="gp">>>> </span><span class="n">Model</span><span class="o">.</span><span class="n">Output</span><span class="o">.</span><span class="n">names</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'A'</span><span class="p">,</span> <span class="s1">'B'</span><span class="p">]</span>
+</pre></div>
+</div>
+<p>With this we have completed an interface to our model.
+We can now evaluate this model on the samples created in the input example.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">output</span><span class="p">,</span> <span class="n">samples</span> <span class="o">=</span> <span class="n">Model</span><span class="o">.</span><span class="n">run_model_parallel</span><span class="p">(</span><span class="n">samples</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Other types of model links can be found in <a class="reference internal" href="examples.html"><span class="doc">EXAMPLES</span></a>, e.g. <a class="reference internal" href="beam.html"><span class="doc">Example: beam</span></a> uses a shell command and parser.</p>
+</section>
+</section>
+
+ </article>
+ </div>
+ <footer>
+
+ <div class="related-pages">
+ <a class="next-page" href="surrogate_description.html">
+ <div class="page-info">
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+ <div class="title">Training surrogate models</div>
+ </div>
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+ <ul>
+<li><a class="reference internal" href="#">Models</a><ul>
+<li><a class="reference internal" href="#example">Example</a></li>
+</ul>
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+</ul>
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diff --git a/docs/build/html/modelcomparison.html b/docs/build/html/modelcomparison.html
index cb7d29e4a94539c7db343358b7ee16b9c99098d6..cf69b3c90c9e5bbc7276120075c6701cf530e389 100644
--- a/docs/build/html/modelcomparison.html
+++ b/docs/build/html/modelcomparison.html
@@ -10,7 +10,7 @@
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@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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-<li class="toctree-l1 current has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
+<li class="toctree-l1 current has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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@@ -175,12 +181,6 @@
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</ul>
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-<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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-<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
-</li>
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diff --git a/docs/build/html/ohaganfunction.html b/docs/build/html/ohaganfunction.html
index 9b8c9ca92055e25ab9060886e9661819515ee1db..4a7174016ebd7e235fc2bbb795f5e4014c1ad2bd 100644
--- a/docs/build/html/ohaganfunction.html
+++ b/docs/build/html/ohaganfunction.html
@@ -10,7 +10,7 @@
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+ <link rel="stylesheet" type="text/css" href="_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="tutorial.html">TUTORIAL</a></li>
-<li class="toctree-l1 current has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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<li class="toctree-l2"><a class="reference internal" href="borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
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-<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
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diff --git a/docs/build/html/pollution.html b/docs/build/html/pollution.html
index 8f462043fbd1f817ff361cc3b3999a6b9234d88c..f04719ba1591837f19b1faf691e2fc656a5a5963 100644
--- a/docs/build/html/pollution.html
+++ b/docs/build/html/pollution.html
@@ -3,14 +3,14 @@
<head><meta charset="utf-8"/>
<meta name="viewport" content="width=device-width,initial-scale=1"/>
<meta name="color-scheme" content="light dark"><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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+ <link rel="stylesheet" type="text/css" href="_static/custom.css?v=3c2b257a" />
@@ -164,8 +164,14 @@
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+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
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- <section id="postprocessing-bayesian-inference-and-bayesian-model-comparison">
-<h1>Postprocessing, Bayesian inference and Bayesian model comparison<a class="headerlink" href="#postprocessing-bayesian-inference-and-bayesian-model-comparison" title="Link to this heading">¶</a></h1>
+ <section id="postprocessing">
+<h1>Postprocessing<a class="headerlink" href="#postprocessing" title="Link to this heading">¶</a></h1>
+<div class="twocol docutils container">
+<div class="leftside docutils container">
+<p>Postprocessing refers to evaluations and checks performed on a model to get an understanding of its properties and estimate its quality.
+The BayesValidRox class <a class="reference internal" href="_autosummary/bayesvalidrox.post_processing.post_processing.PostProcessing.html#bayesvalidrox.post_processing.post_processing.PostProcessing" title="bayesvalidrox.post_processing.post_processing.PostProcessing"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.post_processing.post_processing.PostProcessing</span></code></a> includes functions that are applicable to all types of surrogate model.</p>
+<blockquote>
+<div><ul class="simple">
+<li><p><code class="docutils literal notranslate"><span class="pre">valid_metamodel</span></code>: visualizing some metamodel runs against the corresponding model runs</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">check_accuracy</span></code>: computing the RMSE error of the surrogate model</p></li>
+</ul>
+</div></blockquote>
+</div>
+<div class="rightside docutils container">
+<a class="reference internal image-reference" href="_images/postprocessing.png"><img alt="UML diagram for the classes and functions used in active learning in BayesValidRox." src="_images/postprocessing.png" style="width: 300px;" /></a>
+</div>
+</div>
+<p>Postprocessing methods that are specific to a type of surrogate or training include</p>
+<ul class="simple">
+<li><p><code class="docutils literal notranslate"><span class="pre">plot_moments</span></code>: visualizing the moments of a polynomial chaos expansion (PCE, aPCE)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">sobol_indices</span></code>: calculating the Sobol’ and Total Sobol’ indices (PCE, aPCE)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">plot_seq_design_diagnostics</span></code>: visualizing diagnostics that were evaluated during sequential training (surrogate trained with <code class="docutils literal notranslate"><span class="pre">train_sequential</span></code>)</p></li>
+</ul>
+<section id="example">
+<h2>Example<a class="headerlink" href="#example" title="Link to this heading">¶</a></h2>
+<p>We want to compare out trained surrogate from <a class="reference internal" href="al_description.html"><span class="doc">Active learning: iteratively expanding the training set</span></a> against its original model.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">bayesvalidrox</span> <span class="kn">import</span> <span class="n">PostProcessing</span>
+</pre></div>
+</div>
+<p>The postprocessing object expects the full engine. This allows it to perform both sampling, running the model and running the surrogate model.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">PostProc</span> <span class="o">=</span> <span class="n">PostProcessing</span><span class="p">(</span><span class="n">Engine_</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>To gain an understanding of the approximation quality we use both <code class="docutils literal notranslate"><span class="pre">valid_metamodel</span></code> and <code class="docutils literal notranslate"><span class="pre">check_accuracy</span></code>.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">PostProc</span><span class="o">.</span><span class="n">valid_metamodel</span><span class="p">(</span><span class="n">n_samples</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">PostProc</span><span class="o">.</span><span class="n">check_accuracy</span><span class="p">(</span><span class="n">n_samples</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>The visual comparison of model and metamodel results is saved in the folder <code class="docutils literal notranslate"><span class="pre">Outputs_PostProcessing_calib</span></code>, while the accuracy check is given as console output.</p>
+<div class="twocol docutils container">
+<div class="leftside docutils container">
+<div class="highlight-py notranslate"><div class="highlight"><pre><span></span><span class="go">>>>>> Errors of A <<<<<</span>
+
+<span class="go">Index | RMSE | Validation Error</span>
+<span class="go">-----------------------------------</span>
+<span class="go">1 | 1.513e-07 | 2.224e-15</span>
+
+<span class="go">>>>>> Errors of B <<<<<</span>
+
+<span class="go">Index | RMSE | Validation Error</span>
+<span class="go">-----------------------------------</span>
+<span class="go">1 | 5.045e-05 | 2.406e-11</span>
+</pre></div>
+</div>
+</div>
+<div class="rightside docutils container">
+<a class="reference internal image-reference" href="_images/Model_vs_PCEModel_y_1.pdf"><img alt="Visual comparison of model and metamodel outputs" src="_images/Model_vs_PCEModel_y_1.pdf" style="width: 400px;" /></a>
+</div>
+</div>
+</section>
</section>
</article>
@@ -341,23 +402,23 @@
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diff --git a/docs/build/html/surrogate_description.html b/docs/build/html/surrogate_description.html
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+<li class="toctree-l1 current has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
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@@ -326,7 +328,7 @@
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- <label class="toc-overlay-icon toc-content-icon no-toc" for="__toc">
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@@ -334,6 +336,95 @@
<article role="main">
<section id="training-surrogate-models">
<h1>Training surrogate models<a class="headerlink" href="#training-surrogate-models" title="Link to this heading">¶</a></h1>
+<p>Surrogate models, also called metamodels, are models that are built on evaluations of full models with the goal to capture the full behaviour, but reduce the cost of evaluations.</p>
+<p>In BayesValidRox two types of surrogate model are available, polynomial chaos expansion and Gaussian processes.
+The Polynomial Chaos Expansion (PCE) and its variant the arbitrary Polynomial Chaos Expansion (aPC) build polynomials from the given distributions of uncertain inputs.
+Gaussian processes (GP) give kernel-based representations of the model results.</p>
+<p>The surrogate models are trained on datasets <span class="math notranslate nohighlight">\(\mathcal{D}=(x_i, y_i)_{i=1,\dots,M)\)</span> that consist of <span class="math notranslate nohighlight">\(M\)</span> samples of the uncertain parameters and the corresponding model outputs.
+We call this dataset the training data, with training samples <span class="math notranslate nohighlight">\((x_i)_{i=1,\dots,M)\)</span>.</p>
+<section id="metamodel-and-engine-classes">
+<h2>MetaModel and Engine classes<a class="headerlink" href="#metamodel-and-engine-classes" title="Link to this heading">¶</a></h2>
+<p>BayesValidRox creates surrogate models as objects of the class <a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html#bayesvalidrox.surrogate_models.surrogate_models.MetaModel" title="bayesvalidrox.surrogate_models.surrogate_models.MetaModel"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.surrogate_models.surrogate_models.MetaModel</span></code></a>.
+Training is performed by the class <a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html#bayesvalidrox.surrogate_models.engine.Engine" title="bayesvalidrox.surrogate_models.engine.Engine"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.surrogate_models.engine.Engine</span></code></a>.</p>
+<a class="reference internal image-reference" href="_images/metamod_training_reduced.png"><img alt="UML diagram for metamodel-related classes in bayesvalidrox" src="_images/metamod_training_reduced.png" style="width: 800px;" /></a>
+</section>
+<section id="metamodel-options">
+<h2>MetaModel options<a class="headerlink" href="#metamodel-options" title="Link to this heading">¶</a></h2>
+</section>
+<section id="training-with-the-engine">
+<h2>Training with the engine<a class="headerlink" href="#training-with-the-engine" title="Link to this heading">¶</a></h2>
+<p>For training a surrogate model we use an object of class <a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html#bayesvalidrox.surrogate_models.engine.Engine" title="bayesvalidrox.surrogate_models.engine.Engine"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.surrogate_models.engine.Engine</span></code></a>.
+This needs to be given three things: the metamodel itself, the model that the metamodel should replace and the experimental design that matches the uncertain inputs for the model and metamodel.</p>
+<p>The standard method of training the surrogate is performed by the function <code class="docutils literal notranslate"><span class="pre">train_normal()</span></code>.
+Other available training methods in BayesValidRox are presented in <a class="reference internal" href="al_description.html"><span class="doc">Active learning: iteratively expanding the training set</span></a>.</p>
+<p>For training the engine performs three main steps.</p>
+<ol class="arabic simple">
+<li><p>Generating training samples from the experimental design.</p></li>
+<li><p>Evaluating the model on the training samples.</p></li>
+<li><p>Fitting the surrogate to the training dataset.</p></li>
+</ol>
+</section>
+<section id="example">
+<h2>Example<a class="headerlink" href="#example" title="Link to this heading">¶</a></h2>
+<p>We now build a surrogate model for the simple model from <a class="reference internal" href="model_description.html"><span class="doc">Models</span></a> using the experimental design from <a class="reference internal" href="input_description.html"><span class="doc">Priors, input space and experimental design</span></a>.
+For this we need the classes <a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.surrogate_models.MetaModel.html#bayesvalidrox.surrogate_models.surrogate_models.MetaModel" title="bayesvalidrox.surrogate_models.surrogate_models.MetaModel"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.surrogate_models.surrogate_models.MetaModel</span></code></a> and <a class="reference internal" href="_autosummary/bayesvalidrox.surrogate_models.engine.Engine.html#bayesvalidrox.surrogate_models.engine.Engine" title="bayesvalidrox.surrogate_models.engine.Engine"><code class="xref any py py-class docutils literal notranslate"><span class="pre">bayesvalidrox.surrogate_models.engine.Engine</span></code></a>.</p>
+<p>>> from bayesvalidrox import MetaModel, Engine</p>
+<p>First we set up the surrogate model and tell it to consider the uncertain parameters defined in <code class="docutils literal notranslate"><span class="pre">Inputs</span></code> as its input parameters.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">MetaMod</span> <span class="o">=</span> <span class="n">MetaModel</span><span class="p">(</span><span class="n">Inputs</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Then we specify what type of surrogate we want and its properties.
+Here we use an aPCE with maximal polynomial degree 3 and want to use FastARD as the regression method.
+We set the value of the q-norm truncation scheme to 0.9.
+This combination will give us a sparse aPCE.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">MetaMod</span><span class="o">.</span><span class="n">meta_model_type</span> <span class="o">=</span> <span class="s1">'aPCE'</span>
+<span class="gp">>>> </span><span class="n">MetaMod</span><span class="o">.</span><span class="n">pce_reg_method</span> <span class="o">=</span> <span class="s1">'FastARD'</span>
+<span class="gp">>>> </span><span class="n">MetaMod</span><span class="o">.</span><span class="n">pce_deg</span> <span class="o">=</span> <span class="mi">3</span>
+<span class="gp">>>> </span><span class="n">MetaMod</span><span class="o">.</span><span class="n">pce_q_norm</span> <span class="o">=</span> <span class="mf">0.85</span>
+</pre></div>
+</div>
+<p>Before we start the actual training we need to set some training-related values for the experimental design.
+Most importantly we set the attribute <code class="docutils literal notranslate"><span class="pre">method</span></code> to ‘normal’ to indicate that no iterations are performed during the training and we set <code class="docutils literal notranslate"><span class="pre">n_init_samples</span></code> to our wanted number of training samples.</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>The attribute <code class="docutils literal notranslate"><span class="pre">method</span></code> will be deprecated in further release.</p>
+</div>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">ExpDesign</span><span class="o">.</span><span class="n">method</span> <span class="o">=</span> <span class="s1">'normal'</span>
+<span class="gp">>>> </span><span class="n">ExpDesign</span><span class="o">.</span><span class="n">n_init_samples</span> <span class="o">=</span> <span class="mi">10</span>
+</pre></div>
+</div>
+<p>Like this the experimental design will generate 10 samples according to our previously set sampling method.
+Alternatively we can set the samples that we generated in <a class="reference internal" href="input_description.html"><span class="doc">Priors, input space and experimental design</span></a> as the training samples.
+For this the sampling method should be set to ‘user’ and our samples given as <code class="docutils literal notranslate"><span class="pre">X</span></code>.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">ExpDesign</span><span class="o">.</span><span class="n">sampling_method</span> <span class="o">=</span> <span class="s1">'user'</span>
+<span class="gp">>>> </span><span class="n">ExpDesign</span><span class="o">.</span><span class="n">root_samples</span> <span class="o">=</span> <span class="n">samples</span>
+</pre></div>
+</div>
+<p>Now we create an engine object with the model, experimental design and surrogate model.
+With the function <code class="docutils literal notranslate"><span class="pre">start_engine</span></code> the engine performs its preparations for training.</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>The function start_engine will likely be deprecated in future releases.</p>
+</div>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">Engine_</span> <span class="o">=</span> <span class="n">Engine</span><span class="p">(</span><span class="n">MetaMod</span><span class="p">,</span> <span class="n">Model</span><span class="p">,</span> <span class="n">ExpDesign</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">Engine_</span><span class="o">.</span><span class="n">start_engine</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>Then we train the surrogate model.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">Engine</span><span class="o">.</span><span class="n">train_normal</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>We can evaluate the trained surrogate model in two ways, via the engine, or directly.
+The evaluations return the mean approximation of the surrogate and its associated standard deviation.
+Evaluation via the surrogate model can make use of the sampling in the experimental design,</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">mean</span><span class="p">,</span> <span class="n">stdev</span> <span class="o">=</span> <span class="n">Engine_</span><span class="o">.</span><span class="n">eval_metamodel</span><span class="p">(</span><span class="n">nsamples</span> <span class="o">=</span> <span class="mi">10</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>while for direct evaluation the exact set of samples has to be given.</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">mean</span><span class="p">,</span> <span class="n">stdev</span> <span class="o">=</span> <span class="n">Engine_</span><span class="o">.</span><span class="n">MetaModel</span><span class="o">.</span><span class="n">eval_metamodel</span><span class="p">(</span><span class="n">samples</span><span class="p">)</span>
+</pre></div>
+</div>
+</section>
</section>
</article>
@@ -341,23 +432,23 @@
<footer>
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- <a class="next-page" href="post_description.html">
+ <a class="next-page" href="al_description.html">
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@@ -379,9 +470,31 @@
</footer>
</div>
- <aside class="toc-drawer no-toc">
+ <aside class="toc-drawer">
+ <div class="toc-sticky toc-scroll">
+ <div class="toc-title-container">
+ <span class="toc-title">
+ On this page
+ </span>
+ </div>
+ <div class="toc-tree-container">
+ <div class="toc-tree">
+ <ul>
+<li><a class="reference internal" href="#">Training surrogate models</a><ul>
+<li><a class="reference internal" href="#metamodel-and-engine-classes">MetaModel and Engine classes</a></li>
+<li><a class="reference internal" href="#metamodel-options">MetaModel options</a></li>
+<li><a class="reference internal" href="#training-with-the-engine">Training with the engine</a></li>
+<li><a class="reference internal" href="#example">Example</a></li>
+</ul>
+</li>
+</ul>
+
+ </div>
+ </div>
+ </div>
+
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@@ -389,5 +502,6 @@
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+ <script async="async" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js"></script>
</body>
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\ No newline at end of file
diff --git a/docs/build/html/tutorial.html b/docs/build/html/tutorial.html
index 37771403939c0801b7180b067cbc0c4a01880a96..2cf29844b89f6f00b562f3da8838b7d98a97effb 100644
--- a/docs/build/html/tutorial.html
+++ b/docs/build/html/tutorial.html
@@ -3,7 +3,7 @@
<head><meta charset="utf-8"/>
<meta name="viewport" content="width=device-width,initial-scale=1"/>
<meta name="color-scheme" content="light dark"><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
-<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="EXAMPLES" href="examples.html" /><link rel="prev" title="Surrogate-assisted Bayesian validation of computational models" href="index.html" />
+<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="EXAMPLES" href="examples.html" /><link rel="prev" title="Postprocessing, Bayesian inference and Bayesian model comparison" href="post_description.html" />
<!-- Generated with Sphinx 7.3.7 and Furo 2023.09.10 -->
<title>TUTORIAL - bayesvalidrox 1.0.0 documentation</title>
@@ -164,8 +164,14 @@
</form>
<div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
<ul class="current">
+<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">USER GUIDE</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of USER GUIDE</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
+<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
+</ul>
+</li>
<li class="toctree-l1 current current-page"><a class="current reference internal" href="#">TUTORIAL</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="examples.html">EXAMPLES</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of EXAMPLES</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
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<li class="toctree-l2"><a class="reference internal" href="borehole.html">Borehole</a></li>
@@ -175,12 +181,6 @@
<li class="toctree-l2"><a class="reference internal" href="pollution.html">Pollution</a></li>
</ul>
</li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="packagedescription.html">PACKAGE DESCRIPTION</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of PACKAGE DESCRIPTION</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="input_description.html">Priors, input space and experimental design</a></li>
-<li class="toctree-l2"><a class="reference internal" href="surrogate_description.html">Training surrogate models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="post_description.html">Postprocessing, Bayesian inference and Bayesian model comparison</a></li>
-</ul>
-</li>
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@@ -698,14 +698,14 @@ plots of posterior predictions if wanted.</p>
</div>
<svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
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- <a class="prev-page" href="index.html">
+ <a class="prev-page" href="post_description.html">
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- <div class="title">Home</div>
+ <div class="title">Postprocessing, Bayesian inference and Bayesian model comparison</div>
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diff --git a/docs/source/al_description.rst b/docs/source/al_description.rst
new file mode 100644
index 0000000000000000000000000000000000000000..636fa7877bb9b02fd4512c11459647e3c9a57ef7
--- /dev/null
+++ b/docs/source/al_description.rst
@@ -0,0 +1,8 @@
+Active learning: iteratively expanding the training set
+*******************************************************
+
+
+
+.. image:: ../diagrams/active_learning_reduced.png
+ :width: 550
+ :alt: UML diagram for the classes and functions used in active learning in BayesValidRox.
\ No newline at end of file
diff --git a/docs/source/bayes_description.rst b/docs/source/bayes_description.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2cfd3a6a8c43868b09f404eafdd36594ed9c3c7d
--- /dev/null
+++ b/docs/source/bayes_description.rst
@@ -0,0 +1,7 @@
+Bayesian inference and multi-model comparison
+*********************************************
+
+
+.. image:: ../diagrams/bayesian_validation.png
+ :width: 300
+ :alt: UML diagram for classes related to Bayesian inference and multi-model comparison.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 7b710d3601a334b26e54eb4f82fcd3b13a56f1a9..fc4af832215d462fb1f2135b2273c6aad770641c 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -36,7 +36,8 @@ extensions = [
'sphinx.ext.doctest',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
- 'm2r2'
+ 'm2r2',
+ 'sphinx.ext.mathjax',
]
# Add any paths that contain templates here, relative to this directory.
@@ -47,6 +48,9 @@ templates_path = ['_templates']
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
+# Path for mathjax
+mathjax_path = 'http://cdn.mathjax.org/mathjax/latest/MathJax.js'
+
# -- Options for HTML output -------------------------------------------------
diff --git a/docs/source/model_description.rst b/docs/source/model_description.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f08ea0cd2ab6eb368f290d6121ce2e60fa1d35c8
--- /dev/null
+++ b/docs/source/model_description.rst
@@ -0,0 +1,54 @@
+Models
+******
+
+.. container:: twocol
+
+ .. container:: leftside
+
+ BayesValidRox gives options to create interfaces for a variety of models with the class :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel`.
+
+ Its main function is to run the model on given samples and to read in and contain MC references and observations.
+
+ Models can be defined via python functions, shell commands or as general executables.
+ This allows for the use of BayesValidRox with a broad range of models and easy extension to models that are defined with e.g. UM-Bridge.
+
+ .. container:: rightside
+
+ .. image:: ../diagrams/model.png
+ :width: 150
+ :alt: UML diagram for the bayesvalidrox class :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel`.
+
+Example
+=======
+For this example we use a very simple model that maps the uncertain parameter :math:`X` from the example in :any:`input_description` to two outputs, the original value and its square.
+We define this model as a function ``model`` in a new file ``model.py``.
+This function takes a single realization of the uncertain parameter as a 2-dimensional ``np.array`` and returns a dictionary of model results.
+Here we use the key ``A`` for the sample values and ``B`` for their squares.
+Under the key ``x_values`` a list should be given that is of the same length as each output of the model for a single input.
+The values in this list can denote e.g. timesteps and are used in postprocessing as labels of the x-axis.
+
+>>> def model(sample):
+>>> square = sample*sample
+>>> outputs = {'A': sample, 'B': square, 'x_values': [0]}
+>>> return outputs
+
+In the main python file we can create an object of :any:`bayesvalidrox.pylink.pylink.PyLinkForwardModel` that links to this model.
+
+>>> from bayesvalidrox import PyLinkForwardModel
+
+We create an object of this class and set the ``link_type`` as 'Function' to indicate that this is a function in a python file.
+``py_file`` should be set to the filename of the model and ``name`` to the name of the function.
+Lastly we list the keys of the outputs that we are interested in.
+
+>>> Model = PyLinkForwardModel()
+>>> Model.link_type = 'Function'
+>>> Model.py_file = 'model'
+>>> Model.name = 'model'
+>>> Model.Output.names = ['A', 'B']
+
+With this we have completed an interface to our model.
+We can now evaluate this model on the samples created in the input example.
+
+>>> output, samples = Model.run_model_parallel(samples)
+
+Other types of model links can be found in :any:`examples`, e.g. :any:`beam` uses a shell command and parser.
diff --git a/docs/source/post_description.rst b/docs/source/post_description.rst
index 9950c8cf9ee8a3709506e18b2a68ec51a63f7fd4..af2172709f4581abfabdcfd06257edfa808aa501 100644
--- a/docs/source/post_description.rst
+++ b/docs/source/post_description.rst
@@ -1,2 +1,66 @@
-Postprocessing, Bayesian inference and Bayesian model comparison
-****************************************************************
\ No newline at end of file
+Postprocessing
+**************
+.. container:: twocol
+
+ .. container:: leftside
+
+ Postprocessing refers to evaluations and checks performed on a model to get an understanding of its properties and estimate its quality.
+ The BayesValidRox class :any:`bayesvalidrox.post_processing.post_processing.PostProcessing` includes functions that are applicable to all types of surrogate model.
+
+ * ``valid_metamodel``: visualizing some metamodel runs against the corresponding model runs
+ * ``check_accuracy``: computing the RMSE error of the surrogate model
+
+ .. container:: rightside
+
+ .. image:: ../diagrams/postprocessing.png
+ :width: 300
+ :alt: UML diagram for the classes and functions used in active learning in BayesValidRox.
+
+Postprocessing methods that are specific to a type of surrogate or training include
+
+* ``plot_moments``: visualizing the moments of a polynomial chaos expansion (PCE, aPCE)
+* ``sobol_indices``: calculating the Sobol' and Total Sobol' indices (PCE, aPCE)
+* ``plot_seq_design_diagnostics``: visualizing diagnostics that were evaluated during sequential training (surrogate trained with ``train_sequential``)
+
+
+Example
+=======
+We want to compare out trained surrogate from :any:`al_description` against its original model.
+
+>>> from bayesvalidrox import PostProcessing
+
+The postprocessing object expects the full engine. This allows it to perform both sampling, running the model and running the surrogate model.
+
+>>> PostProc = PostProcessing(Engine_)
+
+To gain an understanding of the approximation quality we use both ``valid_metamodel`` and ``check_accuracy``.
+
+>>> PostProc.valid_metamodel(n_samples=1)
+>>> PostProc.check_accuracy(n_samples=10)
+
+The visual comparison of model and metamodel results is saved in the folder ``Outputs_PostProcessing_calib``, while the accuracy check is given as console output.
+
+.. container:: twocol
+
+ .. container:: leftside
+
+ .. code-block:: py
+
+ >>>>> Errors of A <<<<<
+
+ Index | RMSE | Validation Error
+ -----------------------------------
+ 1 | 1.513e-07 | 2.224e-15
+
+ >>>>> Errors of B <<<<<
+
+ Index | RMSE | Validation Error
+ -----------------------------------
+ 1 | 5.045e-05 | 2.406e-11
+
+ .. container:: rightside
+
+ .. image:: ../../examples/user_guide/Outputs_PostProcessing_calib/Model_vs_PCEModel_y_1.pdf
+ :width: 400
+ :alt: Visual comparison of model and metamodel outputs
+
\ No newline at end of file
diff --git a/docs/source/surrogate_description.rst b/docs/source/surrogate_description.rst
index 676b73ba6599039c68c3b5c6830645f3e9793fb2..3b32fbe2eeea9fcdeb4d726d806bee68268c902f 100644
--- a/docs/source/surrogate_description.rst
+++ b/docs/source/surrogate_description.rst
@@ -1,2 +1,98 @@
Training surrogate models
-*************************
\ No newline at end of file
+*************************
+Surrogate models, also called metamodels, are models that are built on evaluations of full models with the goal to capture the full behaviour, but reduce the cost of evaluations.
+
+In BayesValidRox two types of surrogate model are available, polynomial chaos expansion and Gaussian processes.
+The Polynomial Chaos Expansion (PCE) and its variant the arbitrary Polynomial Chaos Expansion (aPC) build polynomials from the given distributions of uncertain inputs.
+Gaussian processes (GP) give kernel-based representations of the model results.
+
+The surrogate models are trained on datasets :math:`\mathcal{D}=(x_i, y_i)_{i=1,\dots,M)` that consist of :math:`M` samples of the uncertain parameters and the corresponding model outputs.
+We call this dataset the training data, with training samples :math:`(x_i)_{i=1,\dots,M)`.
+
+
+MetaModel and Engine classes
+============================
+BayesValidRox creates surrogate models as objects of the class :any:`bayesvalidrox.surrogate_models.surrogate_models.MetaModel`.
+Training is performed by the class :any:`bayesvalidrox.surrogate_models.engine.Engine`.
+
+.. image:: ../diagrams/metamod_training_reduced.png
+ :width: 800
+ :alt: UML diagram for metamodel-related classes in bayesvalidrox
+
+MetaModel options
+=================
+
+
+Training with the engine
+========================
+For training a surrogate model we use an object of class :any:`bayesvalidrox.surrogate_models.engine.Engine`.
+This needs to be given three things: the metamodel itself, the model that the metamodel should replace and the experimental design that matches the uncertain inputs for the model and metamodel.
+
+The standard method of training the surrogate is performed by the function ``train_normal()``.
+Other available training methods in BayesValidRox are presented in :any:`al_description`.
+
+For training the engine performs three main steps.
+
+1) Generating training samples from the experimental design.
+2) Evaluating the model on the training samples.
+3) Fitting the surrogate to the training dataset.
+
+Example
+=======
+We now build a surrogate model for the simple model from :any:`model_description` using the experimental design from :any:`input_description`.
+For this we need the classes :any:`bayesvalidrox.surrogate_models.surrogate_models.MetaModel` and :any:`bayesvalidrox.surrogate_models.engine.Engine`.
+
+>> from bayesvalidrox import MetaModel, Engine
+
+First we set up the surrogate model and tell it to consider the uncertain parameters defined in ``Inputs`` as its input parameters.
+
+>>> MetaMod = MetaModel(Inputs)
+
+Then we specify what type of surrogate we want and its properties.
+Here we use an aPCE with maximal polynomial degree 3 and want to use FastARD as the regression method.
+We set the value of the q-norm truncation scheme to 0.9.
+This combination will give us a sparse aPCE.
+
+>>> MetaMod.meta_model_type = 'aPCE'
+>>> MetaMod.pce_reg_method = 'FastARD'
+>>> MetaMod.pce_deg = 3
+>>> MetaMod.pce_q_norm = 0.85
+
+Before we start the actual training we need to set some training-related values for the experimental design.
+Most importantly we set the attribute ``method`` to 'normal' to indicate that no iterations are performed during the training and we set ``n_init_samples`` to our wanted number of training samples.
+
+.. warning::
+ The attribute ``method`` will be deprecated in further release.
+
+>>> ExpDesign.method = 'normal'
+>>> ExpDesign.n_init_samples = 10
+
+Like this the experimental design will generate 10 samples according to our previously set sampling method.
+Alternatively we can set the samples that we generated in :any:`input_description` as the training samples.
+For this the sampling method should be set to 'user' and our samples given as ``X``.
+
+>>> ExpDesign.sampling_method = 'user'
+>>> ExpDesign.root_samples = samples
+
+Now we create an engine object with the model, experimental design and surrogate model.
+With the function ``start_engine`` the engine performs its preparations for training.
+
+.. warning::
+ The function start_engine will likely be deprecated in future releases.
+
+>>> Engine_ = Engine(MetaMod, Model, ExpDesign)
+>>> Engine_.start_engine()
+
+Then we train the surrogate model.
+
+>>> Engine.train_normal()
+
+We can evaluate the trained surrogate model in two ways, via the engine, or directly.
+The evaluations return the mean approximation of the surrogate and its associated standard deviation.
+Evaluation via the surrogate model can make use of the sampling in the experimental design,
+
+>>> mean, stdev = Engine_.eval_metamodel(nsamples = 10)
+
+while for direct evaluation the exact set of samples has to be given.
+
+>>> mean, stdev = Engine_.MetaModel.eval_metamodel(samples)
diff --git a/examples/user_guide/model.py b/examples/user_guide/model.py
new file mode 100644
index 0000000000000000000000000000000000000000..2bb1b011fae7c82bf299f4a92ba6787dd58a0f2b
--- /dev/null
+++ b/examples/user_guide/model.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+"""
+A simple model example for the BVR user guide.
+
+@author: Rebecca Kohlhaas
+"""
+import numpy as np
+
+def model(samples):
+ samples = samples[0]
+ square = np.power(samples, 2)
+ outputs = {'A': samples, 'B': square, 'x_values': [0]}
+ return outputs
\ No newline at end of file