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Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 7] #19

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Merged
merged 4 commits into from
Feb 7, 2021
Merged

Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 7] #19

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a257fb0
:art: Update plots from pymc to arviz dependencies & replace param sd…
CloudChaoszero Jan 19, 2021
1f810d9
:bug: Run complete MLDA Gravity Surv. file w/error
CloudChaoszero Feb 4, 2021
a92d073
:art: Update notebook to run under arviz dependency and cores=1 pm.sa…
CloudChaoszero Feb 7, 2021
72c74f0
:art: Utilize from_pymc() with arviz summary and update notebook
CloudChaoszero Feb 7, 2021
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10 changes: 3 additions & 7 deletions examples/samplers/DEMetropolisZ_EfficiencyComparison.ipynb
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Expand Up @@ -451,9 +451,7 @@
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -530,9 +528,7 @@
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -1373,7 +1369,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.10"
"version": "3.8.5"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
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13 changes: 2 additions & 11 deletions examples/samplers/DEMetropolisZ_tune_drop_fraction.ipynb
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Expand Up @@ -127,9 +127,7 @@
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"name": "stderr",
Expand Down Expand Up @@ -1387,13 +1385,6 @@
"%load_ext watermark\n",
"%watermark -n -u -v -iv -w"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -1412,7 +1403,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.10"
"version": "3.8.5"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
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112 changes: 56 additions & 56 deletions examples/samplers/GLM-hierarchical-jax.ipynb
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1,273 changes: 58 additions & 1,215 deletions examples/samplers/MLDA_gravity_surveying.ipynb
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2 changes: 1 addition & 1 deletion examples/samplers/MLDA_introduction.ipynb
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Expand Up @@ -109,7 +109,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.9"
"version": "3.8.5"
}
},
"nbformat": 4,
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163 changes: 62 additions & 101 deletions examples/samplers/MLDA_simple_linear_regression.ipynb
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10 changes: 5 additions & 5 deletions examples/samplers/MLDA_variance_reduction_linear_regression.ipynb
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Expand Up @@ -533,7 +533,7 @@
}
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@twiecki twiecki Jan 29, 2021 •
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Should probably add the model context to this and below to future proof this and get rid of the annoying warning.


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Sounds great. I quite didn't understand what the FutureWarning recommended, but I am happy to update the description as a PR.

Here was my take on what the FutureWarning recommended haha:

with model:
    trace2_az = az.from_pymc3(trace2)
az.summary(trace2_az)

],
"source": [
"pm.stats.summary(trace1)"
"az.summary(trace1)"
]
},
{
Expand Down Expand Up @@ -632,7 +632,7 @@
}
],
"source": [
"pm.stats.summary(trace2)"
"az.summary(trace2)"
]
},
{
Expand Down Expand Up @@ -680,7 +680,7 @@
}
],
"source": [
"pm.plots.traceplot(trace1)"
"az.plot_trace(trace1)"
]
},
{
Expand Down Expand Up @@ -721,7 +721,7 @@
}
],
"source": [
"pm.plots.traceplot(trace2)"
"az.plot_trace(trace2)"
]
},
{
Expand Down Expand Up @@ -1137,7 +1137,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.9"
"version": "3.8.5"
}
},
"nbformat": 4,
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10 changes: 5 additions & 5 deletions examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb
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Expand Up @@ -136,8 +136,8 @@
],
"source": [
"with pm.Model() as example:\n",
" a = pm.Normal(\"a\", mu=0, sd=5)\n",
" b = pm.HalfNormal(\"b\", sd=1)\n",
" a = pm.Normal(\"a\", mu=0, sigma=5)\n",
" b = pm.HalfNormal(\"b\", sigma=1)\n",
" s = pm.Simulator(\"s\", normal_sim, params=(a, b), sum_stat=\"sort\", epsilon=1, observed=data)\n",
"\n",
" trace, sim_data = pm.sample_smc(kernel=\"ABC\", parallel=True, save_sim_data=True)\n",
Expand Down Expand Up @@ -509,9 +509,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python (PyMC3 Dev)",
"language": "python",
"name": "python3"
"name": "pymc3-dev"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -523,7 +523,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion examples/samplers/SMC2_gaussians.ipynb
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Expand Up @@ -444,7 +444,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
Expand Down