Run CmdStan's stansummary and diagnose utilities. These are
documented in the CmdStan Guide:
https://mc-stan.org/docs/cmdstan-guide/stansummary.html
https://mc-stan.org/docs/cmdstan-guide/diagnose.html
Although these methods can be used for models fit using the
$variational() method, much of the output is
currently only relevant for models fit using the
$sample() method.
See the $summary() for computing similar summaries in R rather than calling CmdStan's utilites.
cmdstan_summary(flags = NULL)
cmdstan_diagnose()An optional character vector of flags (e.g.
flags = c("--sig_figs=1")).
# \dontrun{
fit <- cmdstanr_example("logistic")
fit$cmdstan_diagnose()
#> Processing csv files: /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/logistic-202407021533-1-42dde2.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/logistic-202407021533-2-42dde2.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/logistic-202407021533-3-42dde2.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpiACQ3q/logistic-202407021533-4-42dde2.csv
#>
#> Checking sampler transitions treedepth.
#> Treedepth satisfactory for all transitions.
#>
#> Checking sampler transitions for divergences.
#> No divergent transitions found.
#>
#> Checking E-BFMI - sampler transitions HMC potential energy.
#> E-BFMI satisfactory.
#>
#> Effective sample size satisfactory.
#>
#> Split R-hat values satisfactory all parameters.
#>
#> Processing complete, no problems detected.
fit$cmdstan_summary()
#> Inference for Stan model: logistic_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 (0.043, 0.046, 0.042, 0.041) seconds, 0.17 seconds total
#> Sampling took (0.15, 0.15, 0.16, 0.15) seconds, 0.61 seconds total
#>
#> Mean MCSE StdDev 5% 50% 95% N_Eff N_Eff/s R_hat
#>
#> lp__ -6.6e+01 3.3e-02 1.4 -69 -6.6e+01 -6.4e+01 1837 3007 1.0
#> accept_stat__ 0.90 0.011 0.12 0.65 0.94 1.0 123 202 1.0e+00
#> stepsize__ 0.77 0.038 0.054 0.73 0.77 0.86 2.0 3.3 1.9e+13
#> treedepth__ 2.3 0.10 0.51 2.0 2.0 3.0 26 42 1.1e+00
#> n_leapfrog__ 4.9 0.35 2.0 3.0 3.0 7.0 34 55 1.0e+00
#> divergent__ 0.00 nan 0.00 0.00 0.00 0.00 nan nan nan
#> energy__ 68 0.049 2.0 65 68 72 1652 2704 1.0e+00
#>
#> alpha 3.8e-01 3.5e-03 0.22 0.023 3.8e-01 7.4e-01 3919 6414 1.0
#> beta[1] -6.7e-01 3.8e-03 0.25 -1.1 -6.7e-01 -2.6e-01 4387 7180 1.0
#> beta[2] -2.7e-01 3.5e-03 0.23 -0.64 -2.7e-01 1.1e-01 4209 6889 1.00
#> beta[3] 6.8e-01 4.3e-03 0.26 0.25 6.7e-01 1.1e+00 3682 6026 1.00
#> log_lik[1] -5.1e-01 1.5e-03 0.099 -0.69 -5.1e-01 -3.6e-01 4109 6725 1.0
#> log_lik[2] -4.0e-01 2.2e-03 0.15 -0.67 -3.8e-01 -2.0e-01 4736 7751 1.0
#> log_lik[3] -5.0e-01 3.4e-03 0.22 -0.90 -4.6e-01 -2.0e-01 4043 6617 1.0
#> log_lik[4] -4.5e-01 2.4e-03 0.15 -0.73 -4.3e-01 -2.4e-01 3941 6450 1.0
#> log_lik[5] -1.2e+00 4.5e-03 0.28 -1.7 -1.2e+00 -7.7e-01 3844 6291 1.00
#> log_lik[6] -5.9e-01 2.9e-03 0.19 -0.93 -5.7e-01 -3.2e-01 4123 6748 1.00
#> log_lik[7] -6.4e-01 1.9e-03 0.13 -0.87 -6.3e-01 -4.5e-01 4625 7569 1.0
#> log_lik[8] -2.8e-01 2.1e-03 0.13 -0.53 -2.5e-01 -1.1e-01 3984 6520 1.00
#> log_lik[9] -6.9e-01 2.6e-03 0.17 -0.99 -6.8e-01 -4.4e-01 4294 7028 1.0
#> log_lik[10] -7.4e-01 3.7e-03 0.23 -1.2 -7.1e-01 -4.0e-01 3964 6488 1.0
#> log_lik[11] -2.8e-01 2.1e-03 0.12 -0.51 -2.6e-01 -1.2e-01 3501 5729 1.00
#> log_lik[12] -5.0e-01 3.5e-03 0.23 -0.93 -4.6e-01 -1.9e-01 4348 7116 1.0
#> log_lik[13] -6.6e-01 3.2e-03 0.21 -1.0 -6.3e-01 -3.5e-01 4224 6914 1.00
#> log_lik[14] -3.6e-01 2.7e-03 0.17 -0.68 -3.3e-01 -1.3e-01 4013 6568 1.0
#> log_lik[15] -2.8e-01 1.8e-03 0.11 -0.47 -2.6e-01 -1.3e-01 3538 5790 1.00
#> log_lik[16] -2.8e-01 1.4e-03 0.086 -0.43 -2.7e-01 -1.5e-01 3558 5822 1.00
#> log_lik[17] -1.6e+00 4.8e-03 0.29 -2.1 -1.6e+00 -1.2e+00 3654 5981 1.0
#> log_lik[18] -4.8e-01 1.6e-03 0.11 -0.67 -4.7e-01 -3.1e-01 4457 7294 1.00
#> log_lik[19] -2.3e-01 1.2e-03 0.075 -0.37 -2.3e-01 -1.2e-01 3731 6107 1.00
#> log_lik[20] -1.1e-01 1.4e-03 0.080 -0.26 -9.3e-02 -2.7e-02 3471 5681 1.0
#> log_lik[21] -2.1e-01 1.5e-03 0.086 -0.37 -2.0e-01 -9.3e-02 3393 5554 1.00
#> log_lik[22] -5.7e-01 2.3e-03 0.15 -0.83 -5.6e-01 -3.5e-01 4157 6803 1.00
#> log_lik[23] -3.3e-01 2.1e-03 0.14 -0.60 -3.1e-01 -1.4e-01 4351 7120 1.00
#> log_lik[24] -1.4e-01 1.1e-03 0.066 -0.26 -1.2e-01 -5.2e-02 3635 5949 1.00
#> log_lik[25] -4.6e-01 1.8e-03 0.12 -0.68 -4.5e-01 -2.8e-01 4638 7591 1.0
#> log_lik[26] -1.5e+00 5.1e-03 0.34 -2.1 -1.5e+00 -1.0e+00 4383 7173 1.00
#> log_lik[27] -3.1e-01 2.0e-03 0.12 -0.52 -2.9e-01 -1.4e-01 3553 5815 1.00
#> log_lik[28] -4.4e-01 1.3e-03 0.083 -0.59 -4.4e-01 -3.2e-01 4086 6688 1.0
#> log_lik[29] -7.3e-01 3.4e-03 0.23 -1.1 -7.0e-01 -3.9e-01 4476 7326 1.00
#> log_lik[30] -6.9e-01 2.9e-03 0.19 -1.0 -6.8e-01 -4.1e-01 4511 7383 1.0
#> log_lik[31] -4.9e-01 2.6e-03 0.16 -0.78 -4.7e-01 -2.6e-01 3899 6381 1.00
#> log_lik[32] -4.2e-01 1.8e-03 0.11 -0.61 -4.1e-01 -2.7e-01 3671 6009 1.00
#> log_lik[33] -4.1e-01 1.9e-03 0.13 -0.65 -4.0e-01 -2.3e-01 4622 7564 1.0
#> log_lik[34] -6.4e-02 8.5e-04 0.050 -0.16 -5.0e-02 -1.3e-02 3474 5686 1.00
#> log_lik[35] -5.9e-01 2.6e-03 0.18 -0.92 -5.7e-01 -3.2e-01 4937 8080 1.00
#> log_lik[36] -3.2e-01 1.9e-03 0.13 -0.57 -3.1e-01 -1.5e-01 4737 7753 1.00
#> log_lik[37] -7.0e-01 3.5e-03 0.23 -1.1 -6.7e-01 -3.7e-01 4158 6805 1.0
#> log_lik[38] -3.1e-01 2.4e-03 0.15 -0.60 -2.9e-01 -1.2e-01 4035 6604 1.00
#> log_lik[39] -1.8e-01 1.8e-03 0.11 -0.39 -1.5e-01 -5.2e-02 3644 5964 1.0
#> log_lik[40] -6.8e-01 1.9e-03 0.13 -0.91 -6.7e-01 -4.8e-01 4470 7316 1.0
#> log_lik[41] -1.1e+00 4.1e-03 0.25 -1.6 -1.1e+00 -7.6e-01 3765 6162 1.00
#> log_lik[42] -9.3e-01 3.0e-03 0.20 -1.3 -9.1e-01 -6.3e-01 4354 7127 1.0
#> log_lik[43] -4.1e-01 3.7e-03 0.26 -0.91 -3.5e-01 -1.0e-01 4788 7836 1.00
#> log_lik[44] -1.2e+00 3.1e-03 0.19 -1.5 -1.2e+00 -8.9e-01 3623 5929 1.0
#> log_lik[45] -3.6e-01 1.8e-03 0.12 -0.57 -3.4e-01 -1.9e-01 4021 6581 1.0
#> log_lik[46] -5.8e-01 1.9e-03 0.13 -0.81 -5.7e-01 -3.9e-01 4786 7833 1.0
#> log_lik[47] -3.1e-01 2.0e-03 0.13 -0.55 -2.9e-01 -1.4e-01 4246 6949 1.0
#> log_lik[48] -3.2e-01 1.3e-03 0.082 -0.47 -3.2e-01 -2.0e-01 4166 6819 1.00
#> log_lik[49] -3.2e-01 1.3e-03 0.079 -0.46 -3.1e-01 -2.0e-01 3546 5804 1.00
#> log_lik[50] -1.3e+00 4.9e-03 0.33 -1.9 -1.3e+00 -8.0e-01 4492 7352 1.00
#> log_lik[51] -2.9e-01 1.4e-03 0.093 -0.46 -2.8e-01 -1.6e-01 4451 7284 1.00
#> log_lik[52] -8.4e-01 2.2e-03 0.14 -1.1 -8.3e-01 -6.2e-01 4245 6948 1.0
#> log_lik[53] -4.0e-01 2.1e-03 0.13 -0.63 -3.9e-01 -2.2e-01 3748 6134 1.00
#> log_lik[54] -3.7e-01 2.2e-03 0.14 -0.63 -3.5e-01 -1.7e-01 4130 6759 1.0
#> log_lik[55] -3.9e-01 2.0e-03 0.14 -0.64 -3.7e-01 -2.0e-01 4649 7608 1.0
#> log_lik[56] -3.2e-01 2.8e-03 0.19 -0.69 -2.8e-01 -9.5e-02 4610 7546 1.00
#> log_lik[57] -6.6e-01 1.8e-03 0.12 -0.86 -6.5e-01 -4.7e-01 4203 6879 1.0
#> log_lik[58] -9.5e-01 5.3e-03 0.36 -1.6 -9.0e-01 -4.4e-01 4498 7362 1.00
#> log_lik[59] -1.4e+00 5.4e-03 0.34 -2.0 -1.3e+00 -8.4e-01 4097 6706 1.0
#> log_lik[60] -9.8e-01 2.5e-03 0.16 -1.3 -9.7e-01 -7.3e-01 4050 6628 1.0
#> log_lik[61] -5.4e-01 1.5e-03 0.098 -0.71 -5.3e-01 -3.9e-01 4382 7171 1.0
#> log_lik[62] -8.8e-01 4.7e-03 0.31 -1.4 -8.4e-01 -4.4e-01 4166 6818 1.00
#> log_lik[63] -1.2e-01 1.2e-03 0.072 -0.25 -1.0e-01 -3.2e-02 3346 5477 1.00
#> log_lik[64] -9.0e-01 3.7e-03 0.25 -1.4 -8.8e-01 -5.3e-01 4389 7183 1.00
#> log_lik[65] -2.0e+00 9.9e-03 0.58 -3.0 -2.0e+00 -1.1e+00 3440 5629 1.00
#> log_lik[66] -5.1e-01 2.2e-03 0.14 -0.75 -5.0e-01 -3.1e-01 3804 6226 1.00
#> log_lik[67] -2.8e-01 1.3e-03 0.081 -0.42 -2.7e-01 -1.6e-01 4007 6558 1.00
#> log_lik[68] -1.1e+00 3.7e-03 0.24 -1.5 -1.0e+00 -7.0e-01 4155 6800 1.00
#> log_lik[69] -4.3e-01 1.4e-03 0.084 -0.58 -4.3e-01 -3.1e-01 3753 6142 1.00
#> log_lik[70] -6.4e-01 3.5e-03 0.24 -1.1 -6.1e-01 -3.1e-01 4500 7365 1.00
#> log_lik[71] -6.1e-01 3.0e-03 0.21 -0.99 -5.8e-01 -3.1e-01 4571 7481 1.00
#> log_lik[72] -4.6e-01 2.6e-03 0.17 -0.78 -4.4e-01 -2.2e-01 4261 6974 1.00
#> log_lik[73] -1.5e+00 5.8e-03 0.37 -2.1 -1.5e+00 -9.2e-01 4023 6585 1.0
#> log_lik[74] -9.5e-01 3.1e-03 0.20 -1.3 -9.4e-01 -6.5e-01 4106 6721 1.00
#> log_lik[75] -1.1e+00 5.9e-03 0.38 -1.9 -1.1e+00 -5.9e-01 4198 6870 1.00
#> log_lik[76] -3.7e-01 2.2e-03 0.14 -0.63 -3.5e-01 -1.8e-01 3982 6517 1.0
#> log_lik[77] -8.8e-01 2.2e-03 0.14 -1.1 -8.7e-01 -6.6e-01 4043 6618 1.0
#> log_lik[78] -4.8e-01 2.5e-03 0.17 -0.79 -4.6e-01 -2.5e-01 4533 7418 1.00
#> log_lik[79] -7.6e-01 3.0e-03 0.19 -1.1 -7.5e-01 -4.8e-01 4054 6635 1.0
#> log_lik[80] -5.4e-01 2.8e-03 0.19 -0.89 -5.2e-01 -2.7e-01 4782 7827 1.0
#> log_lik[81] -1.6e-01 1.6e-03 0.10 -0.37 -1.4e-01 -4.9e-02 4161 6810 1.0
#> log_lik[82] -2.2e-01 2.1e-03 0.14 -0.49 -1.9e-01 -6.5e-02 4340 7103 1.0
#> log_lik[83] -3.4e-01 1.3e-03 0.081 -0.48 -3.4e-01 -2.2e-01 3663 5996 1.0
#> log_lik[84] -2.7e-01 1.5e-03 0.092 -0.44 -2.6e-01 -1.5e-01 3524 5767 1.00
#> log_lik[85] -1.3e-01 1.3e-03 0.076 -0.28 -1.1e-01 -4.1e-02 3532 5780 1.0
#> log_lik[86] -1.1e+00 4.8e-03 0.32 -1.7 -1.1e+00 -6.6e-01 4283 7011 1.0
#> log_lik[87] -8.2e-01 1.9e-03 0.13 -1.0 -8.2e-01 -6.3e-01 4347 7115 1.0
#> log_lik[88] -7.8e-01 3.7e-03 0.24 -1.2 -7.5e-01 -4.3e-01 4170 6825 1.00
#> log_lik[89] -1.3e+00 5.0e-03 0.32 -1.8 -1.2e+00 -7.9e-01 4012 6566 1.0
#> log_lik[90] -2.6e-01 2.1e-03 0.14 -0.53 -2.4e-01 -9.3e-02 4313 7058 1.00
#> log_lik[91] -3.9e-01 1.9e-03 0.13 -0.63 -3.7e-01 -2.1e-01 4620 7562 1.0
#> log_lik[92] -1.5e+00 5.7e-03 0.34 -2.1 -1.5e+00 -9.8e-01 3518 5758 1.00
#> log_lik[93] -7.4e-01 3.5e-03 0.22 -1.1 -7.2e-01 -4.2e-01 3871 6336 1.00
#> log_lik[94] -3.2e-01 1.4e-03 0.088 -0.48 -3.1e-01 -1.9e-01 3732 6107 1.0
#> log_lik[95] -3.9e-01 1.8e-03 0.11 -0.58 -3.8e-01 -2.3e-01 3830 6269 1.00
#> log_lik[96] -1.6e+00 4.8e-03 0.28 -2.1 -1.6e+00 -1.1e+00 3457 5657 1.0
#> log_lik[97] -4.3e-01 1.5e-03 0.10 -0.61 -4.2e-01 -2.8e-01 4740 7758 1.00
#> log_lik[98] -1.0e+00 5.5e-03 0.37 -1.7 -1.0e+00 -5.1e-01 4582 7499 1.00
#> log_lik[99] -6.9e-01 2.1e-03 0.14 -0.95 -6.8e-01 -4.8e-01 4565 7472 1.0
#> log_lik[100] -3.9e-01 1.5e-03 0.096 -0.56 -3.8e-01 -2.5e-01 4243 6945 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).
# }