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Update SMC-ABC_Lotka-Volterra_example.ipynb #590

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Merged
merged 3 commits into from
Nov 17, 2023
Merged

Update SMC-ABC_Lotka-Volterra_example.ipynb #590

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ad4d93d
Update SMC-ABC_Lotka-Volterra_example.ipynb
PRKramer Nov 15, 2023
e078c9c
Run pre-commit SMC-ABC_Lotka-Volterra_example (#1)
MacroLens Nov 17, 2023
f171270
fix: add time to the plot command in last plot
MacroLens Nov 17, 2023
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130 changes: 89 additions & 41 deletions examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb
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14 changes: 9 additions & 5 deletions examples/samplers/SMC-ABC_Lotka-Volterra_example.myst.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ jupytext:
format_name: myst
format_version: 0.13
kernelspec:
display_name: Python 3.9.7 ('base')
display_name: Python 3 (ipykernel)
language: python
name: python3
---
Expand Down Expand Up @@ -166,8 +166,8 @@ def add_noise(a, b):
# plotting observed data.
observed = add_noise(a, b)
_, ax = plt.subplots(figsize=(12, 4))
ax.plot(observed[:, 0], "x", label="prey")
ax.plot(observed[:, 1], "x", label="predator")
ax.plot(t, observed[:, 0], "x", label="prey")
ax.plot(t, observed[:, 1], "x", label="predator")
ax.set_xlabel("time")
ax.set_ylabel("population")
ax.set_title("Observed data")
Expand Down Expand Up @@ -198,8 +198,8 @@ az.plot_posterior(idata_lv);
# plot results
_, ax = plt.subplots(figsize=(14, 6))
posterior = idata_lv.posterior.stack(samples=("draw", "chain"))
ax.plot(observed[:, 0], "o", label="prey", c="C0", mec="k")
ax.plot(observed[:, 1], "o", label="predator", c="C1", mec="k")
ax.plot(t, observed[:, 0], "o", label="prey", c="C0", mec="k")
ax.plot(t, observed[:, 1], "o", label="predator", c="C1", mec="k")
ax.plot(competition_model(None, posterior["a"].mean(), posterior["b"].mean()), linewidth=3)
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This also needs t as x values

for i in np.random.randint(0, size, 75):
sim = competition_model(None, posterior["a"][i], posterior["b"][i])
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and so do the two plot calls right under this line

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Weird I did run the pre-commit. I'll try again.

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Oops I misinterpreted what you meant. I fixed this in f171270.

Expand All @@ -224,3 +224,7 @@ martin2021bayesian

:::{include} ../page_footer.md
:::

```{code-cell} ipython3

```