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Updated LKJ notebook to PyMC 6 #875

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Updated LKJ notebook to PyMC 6 #875

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493 changes: 350 additions & 143 deletions examples/howto/LKJ.ipynb
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32 changes: 20 additions & 12 deletions examples/howto/LKJ.myst.md
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ outputId: 90631275-86c9-4f4a-f81a-22465d0c8b8c
import arviz as az
import numpy as np
import pymc as pm
import xarray as xr

from matplotlib import pyplot as plt
from matplotlib.lines import Line2D
Expand All @@ -45,7 +46,7 @@ print(f"Running on PyMC v{pm.__version__}")
%config InlineBackend.figure_format = 'retina'
RANDOM_SEED = 8927
rng = np.random.default_rng(RANDOM_SEED)
az.style.use("arviz-darkgrid")
az.style.use("arviz-variat")
```

```{code-cell} ipython3
Expand Down Expand Up @@ -188,6 +189,7 @@ outputId: f039bfb8-1acf-42cb-b054-bc2c97697f96
---
with model:
trace = pm.sample(
nuts_sampler="pymc",
random_seed=rng,
idata_kwargs={"dims": {"chol_stds": ["axis"], "chol_corr": ["axis", "axis_bis"]}},
)
Expand All @@ -208,12 +210,12 @@ colab:
id: dgOKiSLdr2Pi
outputId: a29bde4b-c4dc-49f4-e65d-c3365c1933e1
---
az.plot_trace(
pc = az.plot_dist(
trace,
var_names="chol_corr",
coords={"axis": "y", "axis_bis": "z"},
lines=[("chol_corr", {}, Rho_actual[0, 1])],
);
)
az.add_lines(pc, {"chol_corr": Rho_actual[0, 1]});
```

```{code-cell} ipython3
Expand All @@ -224,16 +226,19 @@ colab:
id: dtBWyd5Jr2Pi
outputId: 94ee6945-a564-487a-e447-3c447057f0bf
---
az.plot_trace(
ref_ds = xr.Dataset(
{
"mu": (("axis",), mu_actual),
"cov": (("axis", "axis_bis"), Sigma_actual),
"chol_stds": (("axis",), sigmas_actual),
},
coords={"axis": ["y", "z"], "axis_bis": ["y", "z"]},
)
pc = az.plot_dist(
trace,
var_names=["~chol", "~chol_corr"],
compact=True,
lines=[
("mu", {}, mu_actual),
("cov", {}, Sigma_actual),
("chol_stds", {}, sigmas_actual),
],
);
)
az.add_lines(pc, ref_ds);
```

+++ {"id": "NnLWJyCMr2Pi"}
Expand Down Expand Up @@ -318,6 +323,9 @@ ax.legend(
);
```

## Authors
- Updated to run on PyMC v6, PyTensor v3, and ArviZ v1 by Chris Fonnesbeck in May 2026

```{code-cell} ipython3
---
colab:
Expand Down
9 changes: 5 additions & 4 deletions pixi.toml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
[project]
[workspace]
authors = ["Chris Fonnesbeck <fonnesbeck@gmail.com>"]
channels = ["conda-forge"]
description = "Add a short description here"
Expand All @@ -10,20 +10,19 @@ version = "0.1.0"

[dependencies]
python = ">=3.13.9,<3.14"
pymc = ">=5.26.1,<6"
pytensor = ">=3.0"
arviz = ">=1.1"
jupyter = ">=1.1.1,<2"
ipykernel = ">=7.1.0,<8"
ipywidgets = ">=8.1.8,<9"
numpy = ">=2.3.5,<3"
arviz = ">=0.22.0,<0.23"
numpyro = ">=0.19.0,<0.20"
seaborn = ">=0.13.2,<0.14"
matplotlib = ">=3.10.8,<4"
pandas = ">=2.3.3,<3"
polars = ">=1.35.2,<2"
esbonio = ">=1.0.0,<2"
watermark = ">=2.5.0,<3"
nutpie = ">=0.16.3,<0.17"
numba = ">=0.62.1,<0.63"
scikit-learn = ">=1.7.2,<2"
blackjax = ">=1.3,<2"
Expand All @@ -32,5 +31,7 @@ bokeh = ">=3.8.1,<4"
plotly = ">=6.5.0,<7"

[pypi-dependencies]
pymc = { git = "https://github.com/pymc-devs/pymc.git", rev = "main" }
nutpie = ">=0.16.9,<0.17"
pymc-extras = ">=0.5.0, <0.6"
kaleido = ">=1.2.0, <2"
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