{ "cells": [ { "cell_type": "markdown", "id": "95177c93", "metadata": {}, "source": [ "# 7 - Compasso de Ulisses" ] }, { "cell_type": "code", "execution_count": 1, "id": "c959eff7", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "\n", "from scipy import stats\n", "\n", "import matplotlib.pyplot as plt\n", "from matplotlib.gridspec import GridSpec\n", "\n", "import pandas as pd\n", "from videpy import Vide\n", "\n", "import networkx as nx\n", "# from causalgraphicalmodels import CausalGraphicalModel\n", "\n", "import stan\n", "import nest_asyncio\n", "\n", "plt.style.use('default')\n", "\n", "plt.rcParams['axes.facecolor'] = 'lightgray'\n", "\n", "# To DAG's\n", "import daft\n", "from causalgraphicalmodels import CausalGraphicalModel" ] }, { "cell_type": "code", "execution_count": 2, "id": "d78c9936", "metadata": {}, "outputs": [], "source": [ "# To running the stan in jupyter notebook\n", "nest_asyncio.apply()" ] }, { "cell_type": "markdown", "id": "387751b9", "metadata": {}, "source": [ "### R Code 7.1 - Pag 194" ] }, { "cell_type": "code", "execution_count": 3, "id": "e3b2396b", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | species | \n", "brain | \n", "mass | \n", "
---|---|---|---|
0 | \n", "afarensis | \n", "438 | \n", "37.0 | \n", "
1 | \n", "africanus | \n", "452 | \n", "35.5 | \n", "
2 | \n", "habilis | \n", "612 | \n", "34.5 | \n", "
3 | \n", "boisei | \n", "521 | \n", "41.5 | \n", "
4 | \n", "rudolfensis | \n", "752 | \n", "55.5 | \n", "
5 | \n", "ergaster | \n", "871 | \n", "61.0 | \n", "
6 | \n", "sapiens | \n", "1350 | \n", "53.5 | \n", "
\n", " | species | \n", "brain | \n", "mass | \n", "mass_std | \n", "brain_std | \n", "
---|---|---|---|---|---|
0 | \n", "afarensis | \n", "438 | \n", "37.0 | \n", "-0.779467 | \n", "0.324444 | \n", "
1 | \n", "africanus | \n", "452 | \n", "35.5 | \n", "-0.917020 | \n", "0.334815 | \n", "
2 | \n", "habilis | \n", "612 | \n", "34.5 | \n", "-1.008722 | \n", "0.453333 | \n", "
3 | \n", "boisei | \n", "521 | \n", "41.5 | \n", "-0.366808 | \n", "0.385926 | \n", "
4 | \n", "rudolfensis | \n", "752 | \n", "55.5 | \n", "0.917020 | \n", "0.557037 | \n", "
5 | \n", "ergaster | \n", "871 | \n", "61.0 | \n", "1.421380 | \n", "0.645185 | \n", "
6 | \n", "sapiens | \n", "1350 | \n", "53.5 | \n", "0.733616 | \n", "1.000000 | \n", "
\n", " | mean | \n", "std | \n", "7.0% | \n", "93.0% | \n", "
---|---|---|---|---|
alpha | \n", "0.53 | \n", "0.11 | \n", "0.31 | \n", "0.71 | \n", "
beta | \n", "0.16 | \n", "0.12 | \n", "-0.06 | \n", "0.37 | \n", "
sigma | \n", "0.27 | \n", "0.12 | \n", "0.12 | \n", "0.46 | \n", "
\n", " | mean | \n", "std | \n", "7.0% | \n", "93.0% | \n", "
---|---|---|---|---|
alpha | \n", "0.58 | \n", "0.25 | \n", "0.06 | \n", "1.00 | \n", "
beta[0] | \n", "0.18 | \n", "0.17 | \n", "-0.13 | \n", "0.47 | \n", "
beta[1] | \n", "-0.07 | \n", "0.26 | \n", "-0.52 | \n", "0.43 | \n", "
sigma | \n", "0.31 | \n", "0.16 | \n", "0.12 | \n", "0.59 | \n", "
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000, beta_dim_0: 5, mu_dim_0: 7)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 7 ... 992 993 994 995 996 997 998 999\n", " * beta_dim_0 (beta_dim_0) int64 0 1 2 3 4\n", " * mu_dim_0 (mu_dim_0) int64 0 1 2 3 4 5 6\n", "Data variables:\n", " alpha (chain, draw) float64 0.7899 0.4723 0.1157 ... 0.7226 1.419\n", " beta (chain, draw, beta_dim_0) float64 -1.853 -0.7106 ... 0.8986\n", " sigma (chain, draw) float64 0.7009 0.3478 0.3989 ... 0.1128 0.1313\n", " mu (chain, draw, mu_dim_0) float64 0.7289 0.2776 ... 0.533 1.005\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.503098\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0\n", " num_chains: 4\n", " num_samples: 1000\n", " num_thin: 1\n", " num_warmup: 1000\n", " save_warmup: 0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000, brain_hat_dim_0: 7)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 ... 993 994 995 996 997 998 999\n", " * brain_hat_dim_0 (brain_hat_dim_0) int64 0 1 2 3 4 5 6\n", "Data variables:\n", " brain_hat (chain, draw, brain_hat_dim_0) float64 -0.6716 ... 1.096\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.659568\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000, brain_dim_0: 7)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 7 ... 993 994 995 996 997 998 999\n", " * brain_dim_0 (brain_dim_0) int64 0 1 2 3 4 5 6\n", "Data variables:\n", " brain (chain, draw, brain_dim_0) float64 -0.7301 -0.5669 ... 1.111\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.614761\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 ... 993 994 995 996 997 998 999\n", "Data variables:\n", " acceptance_rate (chain, draw) float64 0.9942 0.9932 1.0 ... 0.7437 0.6009\n", " step_size (chain, draw) float64 0.02283 0.02283 ... 0.01823 0.01823\n", " tree_depth (chain, draw) int64 6 7 5 4 8 6 5 4 5 ... 5 6 7 7 5 7 8 7 7\n", " n_steps (chain, draw) int64 63 159 31 31 255 ... 47 127 255 255 191\n", " diverging (chain, draw) bool False False False ... False False False\n", " energy (chain, draw) float64 2.459 5.23 0.8842 ... -7.189 -5.73\n", " lp (chain, draw) float64 -1.21 0.03107 2.038 ... 10.68 9.605\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.561999\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0\n", " num_chains: 4\n", " num_samples: 1000\n", " num_thin: 1\n", " num_warmup: 1000\n", " save_warmup: 0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000, beta_dim_0: 5, mu_dim_0: 7)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 7 ... 992 993 994 995 996 997 998 999\n", " * beta_dim_0 (beta_dim_0) int64 0 1 2 3 4\n", " * mu_dim_0 (mu_dim_0) int64 0 1 2 3 4 5 6\n", "Data variables:\n", " alpha (chain, draw) float64 0.7899 0.4723 0.1157 ... 0.7226 1.419\n", " beta (chain, draw, beta_dim_0) float64 -1.853 -0.7106 ... 0.8986\n", " sigma (chain, draw) float64 0.7009 0.3478 0.3989 ... 0.1128 0.1313\n", " mu (chain, draw, mu_dim_0) float64 0.7289 0.2776 ... 0.533 1.005\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.756266\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0\n", " num_chains: 4\n", " num_samples: 1000\n", " num_thin: 1\n", " num_warmup: 1000\n", " save_warmup: 0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000, brain_hat_dim_0: 7)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 ... 993 994 995 996 997 998 999\n", " * brain_hat_dim_0 (brain_hat_dim_0) int64 0 1 2 3 4 5 6\n", "Data variables:\n", " brain_hat (chain, draw, brain_hat_dim_0) float64 -0.6716 ... 1.096\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.902129\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000, brain_dim_0: 7)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 7 ... 993 994 995 996 997 998 999\n", " * brain_dim_0 (brain_dim_0) int64 0 1 2 3 4 5 6\n", "Data variables:\n", " brain (chain, draw, brain_dim_0) float64 -0.7301 -0.5669 ... 1.111\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.855774\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0
<xarray.Dataset>\n", "Dimensions: (chain: 4, draw: 1000)\n", "Coordinates:\n", " * chain (chain) int64 0 1 2 3\n", " * draw (draw) int64 0 1 2 3 4 5 6 ... 993 994 995 996 997 998 999\n", "Data variables:\n", " acceptance_rate (chain, draw) float64 0.9942 0.9932 1.0 ... 0.7437 0.6009\n", " step_size (chain, draw) float64 0.02283 0.02283 ... 0.01823 0.01823\n", " tree_depth (chain, draw) int64 6 7 5 4 8 6 5 4 5 ... 5 6 7 7 5 7 8 7 7\n", " n_steps (chain, draw) int64 63 159 31 31 255 ... 47 127 255 255 191\n", " diverging (chain, draw) bool False False False ... False False False\n", " energy (chain, draw) float64 2.459 5.23 0.8842 ... -7.189 -5.73\n", " lp (chain, draw) float64 -1.21 0.03107 2.038 ... 10.68 9.605\n", "Attributes:\n", " created_at: 2023-08-11T18:53:39.807300\n", " arviz_version: 0.15.1\n", " inference_library: stan\n", " inference_library_version: 3.7.0\n", " num_chains: 4\n", " num_samples: 1000\n", " num_thin: 1\n", " num_warmup: 1000\n", " save_warmup: 0