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Rename pymc3 -> pymc #165

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merged 14 commits into from
Mar 23, 2022
Merged

Rename pymc3 -> pymc #165

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0cd0006
Rename pymc3 -> pymc throughout
fonnesbeck Dec 15, 2021
c002fc4
Merge branch 'master' into pymc_rename
canyon289 Mar 20, 2022
f4cf1fb
fix errors in environment.yml and update README to actually work with…
Mar 20, 2022
e8b4928
Repair "typo" in vampire markdown (#172)
mrwizard82d1 Mar 20, 2022
5089147
Update README.md
canyon289 Mar 20, 2022
60b03a8
Update README.md
canyon289 Mar 20, 2022
c6cdd6f
Merge pull request #173 from pymc-devs/add_bmcp
junpenglao Mar 21, 2022
7e634a5
Rename master to main (#174)
canyon289 Mar 21, 2022
104c47e
Update README.md (#175)
canyon289 Mar 21, 2022
8ffee73
Add bayes_rule env (#176)
canyon289 Mar 21, 2022
a9a346b
Update README.md (#178)
canyon289 Mar 21, 2022
81babb7
Update bayes rules environment (#180)
canyon289 Mar 21, 2022
061ce81
Rename pymc3 -> pymc throughout
fonnesbeck Dec 15, 2021
39dc7fb
Merge branch 'pymc_rename' of github.com:fonnesbeck/resources into py…
fonnesbeck Mar 23, 2022
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2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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# Thank you for opening a pull request!

Please check our [style guide](https://github.com/pymc-devs/pymc3/wiki/PyMC's-Jupyter-Notebook-Style), and also make sure that the notebooks you've modified pass the `pre-commit` checks. If, for example, you modified `notebook1.ipynb` and `notebook2.ipynb`, you could do this by running:
Please check our [style guide](https://github.com/pymc-devs/pymc/wiki/PyMC's-Jupyter-Notebook-Style), and also make sure that the notebooks you've modified pass the `pre-commit` checks. If, for example, you modified `notebook1.ipynb` and `notebook2.ipynb`, you could do this by running:

```bash
pre-commit run --files notebook1.ipynb notebook2.ipynb
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4 changes: 2 additions & 2 deletions BCM/CaseStudies/ExtrasensoryPerception.ipynb
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"import arviz as az\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import scipy as sp\n",
"\n",
"from matplotlib import gridspec\n",
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"output_type": "stream",
"text": [
"arviz 0.7.0\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"scipy 1.3.1\n",
"numpy 1.17.3\n",
"last updated: Mon Apr 27 2020 \n",
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12 changes: 6 additions & 6 deletions BCM/CaseStudies/HeuristicDecisionMaking.ipynb
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"import arviz as az\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import scipy.io as sio\n",
"\n",
"from scipy import stats\n",
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"name": "stderr",
"output_type": "stream",
"text": [
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
" \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
]
},
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"name": "stderr",
"output_type": "stream",
"text": [
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/ipykernel_launcher.py:8: FutureWarning: arrays to stack must be passed as a \"sequence\" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.\n",
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/ipykernel_launcher.py:8: FutureWarning: arrays to stack must be passed as a \"sequence\" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.\n",
" \n"
]
},
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"name": "stderr",
"output_type": "stream",
"text": [
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
" \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
]
},
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"text": [
"numpy 1.18.1\n",
"arviz 0.7.0\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"last updated: Mon Apr 27 2020 \n",
"\n",
"CPython 3.7.7\n",
Expand All @@ -861,7 +861,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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6 changes: 3 additions & 3 deletions BCM/CaseStudies/MemoryRetention.ipynb
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"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import seaborn as sns\n",
"import theano\n",
"\n",
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"name": "stdout",
"output_type": "stream",
"text": [
"pymc3 3.8\n",
"pymc 3.8\n",
"pandas 1.0.3\n",
"arviz 0.7.0\n",
"seaborn 0.10.0\n",
Expand All @@ -1016,7 +1016,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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6 changes: 3 additions & 3 deletions BCM/CaseStudies/MultinomialProcessingTrees.ipynb
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"import arviz as az\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import scipy.special as sp\n",
"import theano\n",
"\n",
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"output_type": "stream",
"text": [
"numpy 1.18.1\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"theano 1.0.4\n",
"arviz 0.7.0\n",
"last updated: Mon Apr 27 2020 \n",
Expand All @@ -878,7 +878,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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6 changes: 3 additions & 3 deletions BCM/CaseStudies/NumberConceptDevelopment.ipynb
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"import arviz as az\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import scipy.io as sio\n",
"import theano\n",
"\n",
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"text": [
"theano 1.0.4\n",
"numpy 1.18.1\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"arviz 0.7.0\n",
"last updated: Mon Apr 27 2020 \n",
"\n",
Expand All @@ -1042,7 +1042,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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8 changes: 4 additions & 4 deletions BCM/CaseStudies/PsychophysicalFunctions.ipynb
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"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import theano\n",
"\n",
"from matplotlib import gridspec\n",
"from pymc3.step_methods.hmc import quadpotential\n",
"from pymc.step_methods.hmc import quadpotential\n",
"from scipy import stats\n",
"from theano import tensor as tt\n",
"\n",
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"numpy 1.18.1\n",
"theano 1.0.4\n",
"arviz 0.7.0\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"pandas 1.0.3\n",
"last updated: Mon Apr 27 2020 \n",
"\n",
Expand All @@ -1187,7 +1187,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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8 changes: 4 additions & 4 deletions BCM/CaseStudies/SignalDetectionTheory.ipynb
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"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import seaborn as sns\n",
"\n",
"from matplotlib.patches import Polygon\n",
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"metadata": {},
"source": [
"### Note from Junpeng Lao\n",
"Sampling using HMC (e.g., in STAN and PyMC3), there are better way to diagnose biased inference [[1]](http://mc-stan.org/documentation/case-studies/divergences_and_bias.html), [[2]](http://pymc-devs.github.io/pymc3/notebooks/Diagnosing_biased_Inference_with_Divergences.html)."
"Sampling using HMC (e.g., in STAN and PyMC), there are better way to diagnose biased inference [[1]](http://mc-stan.org/documentation/case-studies/divergences_and_bias.html), [[2]](http://pymc-devs.github.io/pymc/notebooks/Diagnosing_biased_Inference_with_Divergences.html)."
]
},
{
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"source": [
"As shown above, there are a lot of divergences in the trace, and the energy plot is very different from the energy_diff. This is a strong indication of bias in the estimation, and better reparameterization is needed.\n",
"\n",
"Moreover, the reparameterization, which works better in BUGS/JAGS using Gibbs sampler, actually perform worse using NUTS. Again, this demonstrates that many of the tricks and intuition we got using BUGS/JAGS might not translate to PyMC3 and STAN."
"Moreover, the reparameterization, which works better in BUGS/JAGS using Gibbs sampler, actually perform worse using NUTS. Again, this demonstrates that many of the tricks and intuition we got using BUGS/JAGS might not translate to PyMC and STAN."
]
},
{
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"output_type": "stream",
"name": "stdout",
"text": [
"seaborn 0.11.0\npymc3 3.9.2\npandas 1.0.3\narviz 0.10.0\nnumpy 1.18.2\nlast updated: Mon Nov 23 2020 \n\nCPython 3.8.5\nIPython 7.13.0\nwatermark 2.0.2\n"
"seaborn 0.11.0\npymc 3.9.2\npandas 1.0.3\narviz 0.10.0\nnumpy 1.18.2\nlast updated: Mon Nov 23 2020 \n\nCPython 3.8.5\nIPython 7.13.0\nwatermark 2.0.2\n"
]
}
],
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6 changes: 3 additions & 3 deletions BCM/CaseStudies/TheBARTModelofRiskTaking.ipynb
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"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"\n",
"from scipy import stats\n",
"from theano import tensor as tt\n",
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"text": [
"numpy 1.18.1\n",
"arviz 0.7.0\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"pandas 1.0.3\n",
"last updated: Tue Apr 28 2020 \n",
"\n",
Expand All @@ -481,7 +481,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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10 changes: 5 additions & 5 deletions BCM/CaseStudies/TheGCMModelofCategorization.ipynb
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"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import scipy.io as sio\n",
"import seaborn as sns\n",
"import theano\n",
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"name": "stderr",
"output_type": "stream",
"text": [
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
" \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
]
},
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"name": "stderr",
"output_type": "stream",
"text": [
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
"/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
" \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"pymc3 3.8\n",
"pymc 3.8\n",
"pandas 1.0.3\n",
"numpy 1.18.1\n",
"arviz 0.7.0\n",
Expand All @@ -800,7 +800,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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6 changes: 3 additions & 3 deletions BCM/CaseStudies/TheSIMPLEModelofMemory.ipynb
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"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"\n",
"from scipy import stats\n",
"from theano import tensor as tt\n",
Expand Down Expand Up @@ -830,7 +830,7 @@
"pandas 1.0.3\n",
"numpy 1.18.1\n",
"arviz 0.7.0\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"last updated: Tue Apr 28 2020 \n",
"\n",
"CPython 3.7.7\n",
Expand All @@ -847,7 +847,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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4 changes: 2 additions & 2 deletions BCM/ModelSelection/ComparingBinomialRates.ipynb
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"import arviz as az\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"import theano.tensor as tt\n",
"\n",
"from scipy import stats\n",
Expand Down Expand Up @@ -1246,7 +1246,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"pymc3 3.9.2\n",
"pymc 3.9.2\n",
"numpy 1.18.2\n",
"arviz 0.10.0\n",
"last updated: Thu Nov 19 2020 \n",
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6 changes: 3 additions & 3 deletions BCM/ModelSelection/ComparingGaussianMeans.ipynb
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"import arviz as az\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pymc3 as pm\n",
"import pymc as pm\n",
"\n",
"from scipy import stats\n",
"\n",
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"pandas 1.0.3\n",
"arviz 0.7.0\n",
"numpy 1.18.1\n",
"pymc3 3.8\n",
"pymc 3.8\n",
"last updated: Sat Apr 25 2020 \n",
"\n",
"CPython 3.7.7\n",
Expand All @@ -649,7 +649,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "BCM_pymc3",
"display_name": "BCM_pymc",
"language": "python",
"name": "bcm_pymc3"
},
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