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Converting Chp_15 and Chp_16 to v4 #217

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Converting Chp_15 and Chp_16 to v4 #217

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0853ddd
Converting Chp_15 to v4
yahrMason Nov 17, 2022
8de3eed
pre-commit checks
yahrMason Nov 17, 2022
ee026b9
Updating Chp_16
yahrMason Nov 28, 2022
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1,539 changes: 679 additions & 860 deletions Rethinking_2/Chp_15.ipynb
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1,731 changes: 1,541 additions & 190 deletions Rethinking_2/Chp_16.ipynb
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22 changes: 22 additions & 0 deletions Rethinking_2/Data/Lynx_Hare.csv
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@@ -0,0 +1,22 @@
"Year";"Lynx";"Hare"
1900;4;30
1901;6.1;47.2
1902;9.8;70.2
1903;35.2;77.4
1904;59.4;36.3
1905;41.7;20.6
1906;19;18.1
1907;13;21.4
1908;8.3;22
1909;9.1;25.4
1910;7.4;27.1
1911;8;40.3
1912;12.3;57
1913;19.5;76.6
1914;45.7;52.3
1915;51.1;19.5
1916;29.7;11.2
1917;15.8;7.6
1918;9.7;14.6
1919;10.1;16.2
1920;8.6;24.7
85 changes: 85 additions & 0 deletions Rethinking_2/Data/Panda_nuts.csv
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"chimpanzee";"age";"sex";"hammer";"nuts_opened";"seconds";"help"
11;3;"m";"G";0;61;"N"
11;3;"m";"G";0;37;"N"
18;4;"f";"wood";0;20;"N"
18;4;"f";"G";0;14;"y"
18;4;"f";"L";0;13;"N"
11;4;"m";"Q";0;24;"N"
11;4;"m";"Q";0;30.5;"N"
17;5;"f";"wood";0;135;"N"
7;5;"m";"G";3;24;"N"
1;5;"m";"L";0;13;"N"
22;5;"m";"wood";0;34;"N"
9;6;"m";"G";58;66.5;"N"
9;6;"m";"G";4;5;"N"
9;6;"m";"G";21;24;"N"
9;6;"m";"G";9;20;"N"
9;6;"m";"G";2;6;"N"
9;6;"m";"G";30;42;"N"
9;6;"m";"G";19;43;"N"
9;6;"m";"G";13;26.5;"N"
9;6;"m";"G";6;14;"N"
15;6;"m";"G";11;27;"N"
7;6;"m";"G";1;12;"y"
9;6;"m";"G";2;17;"N"
1;6;"m";"L";0;4;"N"
7;6;"m";"G";1;17;"N"
13;6;"m";"wood";0;17;"N"
13;6;"m";"G";0;15;"N"
7;6;"m";"G";0;12;"y"
13;6;"m";"G";0;23;"y"
7;6;"m";"wood";0;47;"N"
3;7;"f";"G";4;23;"N"
3;7;"f";"L";0;16;"N"
3;7;"f";"L";0;13.5;"N"
19;7;"m";"G";8;16;"N"
9;7;"m";"G";10;23.5;"N"
9;7;"m";"G";11;33;"N"
9;7;"m";"G";1;3;"N"
16;8;"f";"G";4;12;"N"
2;8;"f";"G";2;10.5;"N"
2;8;"f";"G";1;12;"N"
16;8;"f";"G";0;7.5;"N"
16;8;"f";"G";0;32;"N"
9;8;"m";"G";36;38;"N"
19;8;"m";"G";4;9;"y"
9;8;"m";"G";16;13;"N"
9;8;"m";"G";77;59;"N"
9;8;"m";"G";41;40;"N"
19;8;"m";"G";22;36;"N"
9;8;"m";"G";49;51;"N"
19;8;"m";"G";37;60;"N"
19;8;"m";"G";31;71;"y"
19;8;"m";"G";11;14;"N"
9;8;"m";"G";5;10;"N"
19;8;"m";"G";8;33;"y"
9;8;"m";"L";0;11;"N"
4;9;"f";"G";1;4.5;"N"
4;9;"f";"wood";0;17;"N"
9;9;"m";"G";30;47;"N"
9;9;"m";"G";13;24;"N"
9;9;"m";"G";15;34.5;"N"
4;10;"f";"G";0;2.5;"N"
8;11;"f";"G";4;13;"N"
14;12;"f";"G";10;10;"N"
21;13;"f";"G";5;13;"N"
12;13;"m";"G";51;43;"N"
5;13;"m";"G";3;6;"N"
5;13;"m";"G";4;6.5;"N"
20;14;"m";"G";50;50;"N"
20;14;"m";"G";36;48;"N"
20;14;"m";"G";6;14.5;"N"
20;14;"m";"G";3;8.5;"N"
20;14;"m";"G";4;15;"N"
20;14;"m";"G";7;17;"N"
20;15;"m";"G";41;56.5;"N"
10;15;"m";"G";27;33;"N"
6;15;"m";"G";30;36;"N"
20;15;"m";"G";17;42;"N"
20;15;"m";"G";14;23;"N"
6;15;"m";"G";16;20;"N"
10;15;"m";"G";7;12;"N"
10;15;"m";"G";5;12.5;"N"
6;15;"m";"G";8;13;"N"
6;16;"m";"G";24;20;"N"
6;16;"m";"G";25;36;"N"
16 changes: 2 additions & 14 deletions Rethinking_2/README.md
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Expand Up @@ -27,11 +27,11 @@ to install all the dependencies into an isolated environment.

Activate the environment by running:

source activate stat-rethink2-pymc
source activate stat-rethink2-pymc_v4

To use the notebooks you first have to register your new environment as a valid notebook kernel:

python -m ipykernel install --user --name stat-rethink2-pymc3 --display-name "Python 3.10 (stat-rethink2-pymc3)"
python -m ipykernel install --user --name stat-rethink2-pymc_v4 --display-name "Python 3.10 (stat-rethink2-pymc_v4)"

You can start a notebook by running:

Expand All @@ -42,18 +42,6 @@ or use the more modern jupyter lab:
jupyter lab

from the root directory.

## PyMC v4 Updates

Work is on-going to update these notebooks to be compatible with PyMC v4. Currently chapters 2 through 14 have been converted.

If you wish to run these notebooks, please create the v4 environment by running:

conda env create -f environment_v4.yml

and activate it with:

source activate stat-rethink2-pymc_v4

---

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11 changes: 7 additions & 4 deletions Rethinking_2/environment.yml
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@@ -1,4 +1,4 @@
name: stat-rethink2-pymc
name: stat-rethink2-pymc_v4
channels:
- conda-forge
dependencies:
Expand All @@ -7,9 +7,12 @@ dependencies:
- seaborn
- mkl-service
- watermark
- pymc3
- arviz
- theano-pymc
- pymc==4.3.0
- arviz==0.13.0
- aeppl==0.0.38
- aesara==2.8.7
- theano-pymc==1.1.2
- tqdm
- mkl
- mkl-service
- pip
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26 changes: 0 additions & 26 deletions Rethinking_2/environment_v4.yml
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