{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 22: Simulation based calibration and related checks in practice\n", "\n", "[Data set download](https://s3.amazonaws.com/bebi103.caltech.edu/data/singer_transcript_counts.csv)\n", "\n", "
\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"
\\n\"+\n", " \"\\n\"+\n",
" \"from bokeh.resources import INLINE\\n\"+\n",
" \"output_notebook(resources=INLINE)\\n\"+\n",
" \"
\\n\"+\n",
" \"\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"
\\n\"+\n \"\n", " | ground_truth | \n", "rank_statistic | \n", "mean | \n", "sd | \n", "shrinkage | \n", "z_score | \n", "Rhat | \n", "ESS | \n", "ESS_per_iter | \n", "tail_ESS | \n", "tail_ESS_per_iter | \n", "n_divergences | \n", "n_bad_ebfmi | \n", "n_max_treedepth | \n", "warning_code | \n", "L | \n", "trial | \n", "parameter | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "0.418733 | \n", "0 | \n", "1.004741 | \n", "0.004720 | \n", "1.000000 | \n", "124.159304 | \n", "1.002847 | \n", "2063.132436 | \n", "0.515783 | \n", "1795.518948 | \n", "0.448880 | \n", "2 | \n", "0 | \n", "0 | \n", "4 | \n", "4000 | \n", "0 | \n", "alpha | \n", "
1 | \n", "0.193699 | \n", "0 | \n", "1.002572 | \n", "0.002566 | \n", "1.000000 | \n", "315.236969 | \n", "1.000743 | \n", "1938.450809 | \n", "0.484613 | \n", "1478.583786 | \n", "0.369646 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "4000 | \n", "1 | \n", "alpha | \n", "
2 | \n", "22.689700 | \n", "3446 | \n", "20.879789 | \n", "1.709294 | \n", "0.998972 | \n", "-1.058865 | \n", "1.007017 | \n", "579.443127 | \n", "0.144861 | \n", "378.743290 | \n", "0.094686 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "4000 | \n", "2 | \n", "alpha | \n", "
3 | \n", "1.026900 | \n", "2032 | \n", "1.034750 | \n", "0.029606 | \n", "1.000000 | \n", "0.265146 | \n", "1.002357 | \n", "1211.397615 | \n", "0.302849 | \n", "1097.282499 | \n", "0.274321 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "4000 | \n", "3 | \n", "alpha | \n", "
4 | \n", "0.298719 | \n", "0 | \n", "1.003109 | \n", "0.003085 | \n", "1.000000 | \n", "228.290468 | \n", "1.001857 | \n", "1673.597065 | \n", "0.418399 | \n", "1116.781554 | \n", "0.279195 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "4000 | \n", "4 | \n", "alpha | \n", "