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Merged
merged 7 commits into from
Nov 23, 2023
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Update notebook GLM-negative-binomial-regression to pymc v5 #573 #575

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521145f
Add seaborn to the requirements-docs.txt
wesleyboelrijk Sep 16, 2023
48f9fab
Update notebook GLM-negative-binomial-regression to pymc v5
wesleyboelrijk Sep 16, 2023
914e37e
Run pre-commit
wesleyboelrijk Sep 16, 2023
a940a40
Remove unrelated files, sort requirements alphabetically, edit notebo…
wesleyboelrijk Oct 2, 2023
355f744
Add seaborn to notebook extra dependency and remove from requirements…
wesleyboelrijk Oct 16, 2023
9830c49
Merge branch 'main' into pydata_sprint
OriolAbril Nov 23, 2023
ed60c05
get ready to merge
OriolAbril Nov 23, 2023
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1 change: 0 additions & 1 deletion examples/case_studies/nyc_bym.ipynb
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Expand Up @@ -634,7 +634,6 @@
"outputs": [],
"source": [
"with pm.Model(coords=coords) as BYM_model:\n",
"\n",
" # intercept\n",
" beta0 = pm.Normal(\"beta0\", 0, 1)\n",
"\n",
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1 change: 0 additions & 1 deletion examples/case_studies/nyc_bym.myst.md
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Expand Up @@ -319,7 +319,6 @@ Lastly, we'll use a Poisson outcome distribution. The number of traffic accident

```{code-cell} ipython3
with pm.Model(coords=coords) as BYM_model:

# intercept
beta0 = pm.Normal("beta0", 0, 1)

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191 changes: 90 additions & 101 deletions examples/generalized_linear_models/GLM-negative-binomial-regression.ipynb
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16 changes: 10 additions & 6 deletions examples/generalized_linear_models/GLM-negative-binomial-regression.myst.md
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Expand Up @@ -5,21 +5,23 @@ jupytext:
format_name: myst
format_version: 0.13
kernelspec:
display_name: Python 3.9.12 ('pymc-dev-py39')
display_name: pymc-dev
language: python
name: python3
name: pymc-dev
---

(GLM-negative-binomial-regression)=
# GLM: Negative Binomial Regression

:::{post} June, 2022
:::{post} September, 2023
:tags: negative binomial regression, generalized linear model,
:category: beginner
:author: Ian Ozsvald, Abhipsha Das, Benjamin Vincent
:author: Ian Ozsvald, Abhipsha Das, Benjamin Vincent, Wesley Boelrijk
:::

```{code-cell} ipython3
import warnings

import arviz as az
import numpy as np
import pandas as pd
Expand All @@ -30,10 +32,11 @@ from scipy import stats
```

```{code-cell} ipython3
warnings.simplefilter(action="ignore", category=FutureWarning)
RANDOM_SEED = 8927
rng = np.random.default_rng(RANDOM_SEED)

%config InlineBackend.figure_format = 'retina'
%config InlineBackend.figure_format = "retina"
az.style.use("arviz-darkgrid")
```

Expand Down Expand Up @@ -229,10 +232,11 @@ See also, [`bambi's` negative binomial example](https://bambinos.github.io/bambi
- Created by [Ian Ozsvald](https://github.com/ianozsvald)
- Updated by [Abhipsha Das](https://github.com/chiral-carbon) in August 2021
- Updated by [Benjamin Vincent](https://github.com/drbenvincent) to PyMC v4 in June 2022
- Updated by [Wesley Boelrijk](https://github.com/wesleyboelrijk) to PyMC v5 in September 2023

```{code-cell} ipython3
%load_ext watermark
%watermark -n -u -v -iv -w -p pytensor,aeppl,xarray
%watermark -n -u -v -iv -w -p pytensor,xarray
```

:::{include} ../page_footer.md
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2 changes: 0 additions & 2 deletions examples/howto/model_builder.ipynb
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Expand Up @@ -46,7 +46,6 @@
"metadata": {},
"outputs": [],
"source": [

"from typing import Dict, List, Optional, Tuple, Union\n",
"\n",
"import arviz as az\n",
Expand Down Expand Up @@ -206,7 +205,6 @@
" self._generate_and_preprocess_model_data(X_values, y_values)\n",
"\n",
" with pm.Model(coords=self.model_coords) as self.model:\n",
"\n",
" # Create mutable data containers\n",
" x_data = pm.MutableData(\"x_data\", X_values)\n",
" y_data = pm.MutableData(\"y_data\", y_values)\n",
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1 change: 0 additions & 1 deletion examples/howto/model_builder.myst.md
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Expand Up @@ -119,7 +119,6 @@ class LinearModel(ModelBuilder):
self._generate_and_preprocess_model_data(X_values, y_values)

with pm.Model(coords=self.model_coords) as self.model:

# Create mutable data containers
x_data = pm.MutableData("x_data", X_values)
y_data = pm.MutableData("y_data", y_values)
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1 change: 1 addition & 0 deletions requirements-docs.txt
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Expand Up @@ -10,3 +10,4 @@ sphinx-codeautolink
sphinx-notfound-page
matplotlib
sphinxext-rediraffe
seaborn