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Merged
merged 10 commits into from
Dec 19, 2021
Merged

Adapt and run blackbox likelihood tutorial #28

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a10291f
Add numpy version of blackbox likelihood notebook
OriolAbril Jan 23, 2021
ea728a9
edit titles to distinguish the two different versions
OriolAbril Jan 23, 2021
40f7d5c
update numpy version of blackbox likelihood nb
OriolAbril Dec 16, 2021
41de275
add target to custom distribution notebook
OriolAbril Dec 16, 2021
1e471ea
add tags
OriolAbril Dec 16, 2021
2498d46
fix code block syntax
OriolAbril Dec 16, 2021
d2fda7b
rerun and fix section headings
OriolAbril Dec 16, 2021
593df29
move section to right place
OriolAbril Dec 16, 2021
073fe6d
review changes and rename
OriolAbril Dec 19, 2021
ffeeb32
address more review comments
OriolAbril Dec 19, 2021
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12 changes: 9 additions & 3 deletions examples/case_studies/blackbox_external_likelihood.ipynb
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Expand Up @@ -4,7 +4,13 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using a \"black box\" likelihood function"
"(blackbox_external_likelihood)=\n",
"# Using a \"black box\" likelihood function (Cython)\n",
"\n",
":::{note}\n",
"This notebook in part of a set of two twin notebooks that perform the exact same task, this one\n",
"uses Cython whereas {ref}`this other one <blackbox_external_likelihood_numpy>` uses NumPy\n",
":::"
]
},
{
Expand Down Expand Up @@ -818,7 +824,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -832,7 +838,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.9.7"
}
},
"nbformat": 4,
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890 changes: 890 additions & 0 deletions examples/case_studies/blackbox_external_likelihood_numpy.ipynb
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5 changes: 3 additions & 2 deletions examples/pymc3_howto/custom_distribution.ipynb
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Expand Up @@ -4,6 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"(custom_distribution)=\n",
"# Defining a Custom Distribution in PyMC3"
]
},
Expand Down Expand Up @@ -534,7 +535,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -548,7 +549,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.1"
"version": "3.9.7"
}
},
"nbformat": 4,
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5 changes: 3 additions & 2 deletions examples/pymc3_howto/profiling.ipynb
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Expand Up @@ -4,6 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"(profiling)=\n",
"# Profiling\n",
"Sometimes computing the likelihood is not as fast as we would like. Theano provides handy profiling tools which are wrapped in PyMC3 by `model.profile`. This function returns a `ProfileStats` object conveying information about the underlying Theano operations. Here we'll profile the likelihood and gradient for the stochastic volatility example.\n",
"\n",
Expand Down Expand Up @@ -315,7 +316,7 @@
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -329,7 +330,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.3"
"version": "3.9.7"
}
},
"nbformat": 4,
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1 change: 1 addition & 0 deletions examples/table_of_contents_tutorials.js
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Expand Up @@ -16,6 +16,7 @@ Gallery.contents = {
"samplers/DEMetropolisZ_tune_drop_fraction": "Deep dives",
"case_studies/factor_analysis": "Deep dives",
"case_studies/blackbox_external_likelihood": "How-To",
"case_studies/blackbox_external_likelihood_numpy": "How-To",
"pymc3_howto/profiling": "How-To",
"pymc3_howto/howto_debugging": "How-To",
"diagnostics_and_criticism/model_averaging": "How-To",
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