From 78d628f51354b233f47891625c6bed273ab8c3b3 Mon Sep 17 00:00:00 2001 From: Brian Ward Date: Tue, 10 Dec 2024 09:53:45 -0500 Subject: [PATCH] update example output --- src/cmdstan-guide/stansummary.qmd | 58 +++++++++++++++---------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/src/cmdstan-guide/stansummary.qmd b/src/cmdstan-guide/stansummary.qmd index db71d624e..744706752 100644 --- a/src/cmdstan-guide/stansummary.qmd +++ b/src/cmdstan-guide/stansummary.qmd @@ -73,38 +73,38 @@ output files to get the following report: ``` > bin/stansummary eight_*.csv -Input files: eight_1.csv, eight_2.csv, eight_3.csv, eight_4.csv Inference for Stan model: eight_schools_model -4 chains: each with iter=(1000,1000,1000,1000); warmup=(0,0,0,0); thin=(1,1,1,1); 4000 iterations saved. - -Warmup took (0.048, 0.060, 0.047, 0.045) seconds, 0.20 seconds total -Sampling took (0.057, 0.058, 0.061, 0.066) seconds, 0.24 seconds total - - Mean MCSE StdDev 5% 50% 95% N_Eff N_Eff/s R_hat - -lp__ -18 0.33 5.1 -26 -19 -9.1 233 963 1.0 -accept_stat__ 0.88 1.6e-02 0.23 0.21 0.98 1.00 203 838 1.0e+00 -stepsize__ 0.18 2.2e-02 0.031 0.14 0.20 0.22 2.0 8.3 3.9e+13 -treedepth__ 3.8 5.9e-02 0.78 2.0 4.0 5.0 175 724 1.0e+00 -n_leapfrog__ 18 1.3e+00 9.4 7.0 15 31 51 212 1.0e+00 -divergent__ 0.015 4.1e-03 0.12 0.00 0.00 0.00 865 3576 1.0e+00 -energy__ 23 3.4e-01 5.5 13 23 32 258 1066 1.0e+00 - -mu 7.9 0.16 5.1 -0.23 7.9 16 1021 4221 1.0 -theta[1] 12 0.30 8.6 -0.48 11 28 837 3459 1.0 -theta[2] 7.8 0.15 6.4 -2.7 7.7 18 1717 7096 1.00 -theta[3] 6.1 0.19 7.7 -6.5 6.5 18 1684 6958 1.0 -theta[4] 7.5 0.15 6.7 -3.1 7.4 18 2026 8373 1.0 -theta[5] 4.7 0.17 6.4 -6.7 5.3 15 1391 5747 1.00 -theta[6] 5.9 0.16 6.7 -5.8 6.2 16 1673 6915 1.00 -theta[7] 11 0.22 7.0 0.057 10 23 1069 4419 1.0 -theta[8] 8.3 0.20 7.9 -4.2 8.0 22 1503 6209 1.00 -tau 7.2 0.26 5.2 1.5 5.9 17 401 1657 1.0 +4 chains: each with iter=1000; warmup=1000; thin=1; 1000 iterations saved. + +Warmup took (0.031, 0.031, 0.038, 0.031) seconds, 0.13 seconds total +Sampling took (0.032, 0.039, 0.026, 0.029) seconds, 0.13 seconds total + + Mean MCSE StdDev MAD 5% 50% 95% ESS_bulk ESS_tail R_hat + +lp__ -18 0.36 5.3 5.5 -26 -18 -8.7 214 217 1.0 +accept_stat__ 0.80 0.021 0.29 0.068 0.033 0.95 1.00 268 314 1.0 +stepsize__ 0.20 nan 0.040 0.029 0.14 0.21 0.25 nan nan nan +treedepth__ 3.7 0.22 0.88 1.5 2.0 4.0 5.0 26 18 1.1 +n_leapfrog__ 17 3.1 10 12 3.0 15 31 30 21 1.1 +divergent__ 0.022 nan 0.15 0.00 0.00 0.00 0.00 nan nan nan +energy__ 23 0.38 5.7 5.8 13 23 32 223 286 1.0 + +mu 7.9 0.16 5.3 4.9 -0.35 7.9 16 977 472 1.0 +theta[1] 12 0.32 8.8 7.4 -0.19 11 28 727 525 1.0 +theta[2] 7.8 0.17 6.4 6.0 -2.8 7.8 18 1298 2137 1.0 +theta[3] 5.9 0.20 8.1 6.8 -8.0 6.5 18 1493 1720 1.0 +theta[4] 7.5 0.17 6.9 6.3 -3.4 7.6 18 1517 1935 1.0 +theta[5] 4.9 0.20 6.3 6.1 -6.1 5.1 15 998 1357 1.0 +theta[6] 5.8 0.18 6.8 6.1 -6.3 6.2 16 1434 1431 1.0 +theta[7] 11 0.25 7.0 6.4 0.42 10 23 741 562 1.0 +theta[8] 8.6 0.21 8.1 7.2 -3.6 8.3 22 1444 1850 1.0 +tau 7.3 0.31 5.8 4.4 1.5 5.7 18 226 1230 1.0 Samples were drawn using hmc with nuts. -For each parameter, N_Eff is a crude measure of effective sample size, -and R_hat is the potential scale reduction factor on split chains (at -convergence, R_hat=1). +For each parameter, ESS_bulk and ESS_tail measure the effective sample size for the entire sample +(bulk) and for the .05 and .95 tails (tail), +and R_hat measures the potential scale reduction on split chains. At convergence R_hat will be +very close to 1.00. ``` The console output information consists of