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 $summary() for computing similar summaries in R rather than calling CmdStan's utilites.
cmdstan_summary(flags = NULL) cmdstan_diagnose()
flags | An optional character vector of flags (e.g.
|
---|
#> Processing csv files: /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpmzUYEz/logistic-202203181225-1-61aacb.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpmzUYEz/logistic-202203181225-2-61aacb.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpmzUYEz/logistic-202203181225-3-61aacb.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpmzUYEz/logistic-202203181225-4-61aacb.csv #> #> Checking sampler transitions treedepth. #> Treedepth satisfactory for all transitions. #> #> Checking sampler transitions for divergences. #> No divergent transitions found. #> #> Checking E-BFMI - sampler transitions HMC potential energy. #> E-BFMI satisfactory. #> #> Effective sample size satisfactory. #> #> Split R-hat values satisfactory all parameters. #> #> Processing complete, no problems detected.fit$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 (0.034, 0.026, 0.028, 0.048) seconds, 0.14 seconds total #> Sampling took (0.095, 0.084, 0.16, 0.12) seconds, 0.46 seconds total #> #> Mean MCSE StdDev 5% 50% 95% N_Eff N_Eff/s R_hat #> #> lp__ -6.6e+01 3.6e-02 1.5 -69 -6.6e+01 -6.4e+01 1736 3791 1.0 #> accept_stat__ 0.90 3.8e-03 0.11 0.67 0.94 1.0 8.5e+02 1.9e+03 1.0e+00 #> stepsize__ 0.75 3.0e-02 0.043 0.68 0.78 0.79 2.0e+00 4.4e+00 1.6e+13 #> treedepth__ 2.4 6.7e-02 0.53 2.0 2.0 3.0 6.2e+01 1.4e+02 1.0e+00 #> n_leapfrog__ 5.2 2.6e-01 2.0 3.0 7.0 7.0 6.0e+01 1.3e+02 1.0e+00 #> divergent__ 0.00 nan 0.00 0.00 0.00 0.00 nan nan nan #> energy__ 68 5.5e-02 2.1 65 68 72 1.4e+03 3.1e+03 1.0e+00 #> #> alpha 3.8e-01 3.3e-03 0.22 0.026 3.8e-01 7.5e-01 4388 9581 1.00 #> beta[1] -6.7e-01 3.9e-03 0.25 -1.1 -6.6e-01 -2.6e-01 4345 9487 1.00 #> beta[2] -2.7e-01 3.6e-03 0.23 -0.66 -2.7e-01 1.1e-01 4144 9048 1.00 #> beta[3] 6.8e-01 4.2e-03 0.27 0.26 6.7e-01 1.1e+00 3965 8656 1.0 #> log_lik[1] -5.1e-01 1.5e-03 0.10 -0.69 -5.1e-01 -3.6e-01 4462 9742 1.00 #> log_lik[2] -4.0e-01 2.2e-03 0.15 -0.68 -3.9e-01 -1.9e-01 4523 9876 1.00 #> log_lik[3] -4.9e-01 3.3e-03 0.22 -0.91 -4.6e-01 -2.0e-01 4388 9582 1.00 #> log_lik[4] -4.5e-01 2.4e-03 0.15 -0.72 -4.3e-01 -2.4e-01 3964 8655 1.00 #> log_lik[5] -1.2e+00 4.2e-03 0.28 -1.7 -1.2e+00 -7.6e-01 4456 9730 1.00 #> log_lik[6] -5.9e-01 2.9e-03 0.19 -0.94 -5.7e-01 -3.2e-01 4286 9359 1.0 #> log_lik[7] -6.4e-01 1.8e-03 0.12 -0.85 -6.4e-01 -4.6e-01 4658 10170 1.00 #> log_lik[8] -2.8e-01 2.3e-03 0.14 -0.54 -2.5e-01 -1.0e-01 3596 7851 1.00 #> log_lik[9] -6.9e-01 2.5e-03 0.17 -0.99 -6.8e-01 -4.5e-01 4349 9495 1.0 #> log_lik[10] -7.3e-01 3.7e-03 0.24 -1.2 -7.1e-01 -3.9e-01 4199 9168 1.00 #> log_lik[11] -2.8e-01 2.0e-03 0.12 -0.51 -2.6e-01 -1.1e-01 3817 8334 1.0 #> log_lik[12] -5.0e-01 3.6e-03 0.24 -0.96 -4.6e-01 -1.8e-01 4375 9553 1.0 #> log_lik[13] -6.6e-01 3.0e-03 0.20 -1.0 -6.4e-01 -3.6e-01 4601 10046 1.0 #> log_lik[14] -3.6e-01 2.7e-03 0.18 -0.69 -3.3e-01 -1.3e-01 4218 9210 1.00 #> log_lik[15] -2.8e-01 1.6e-03 0.11 -0.47 -2.6e-01 -1.3e-01 4392 9589 1.00 #> log_lik[16] -2.8e-01 1.4e-03 0.088 -0.43 -2.7e-01 -1.5e-01 3712 8105 1.00 #> log_lik[17] -1.6e+00 5.0e-03 0.30 -2.1 -1.6e+00 -1.1e+00 3489 7618 1.00 #> log_lik[18] -4.8e-01 1.7e-03 0.11 -0.67 -4.7e-01 -3.2e-01 3930 8582 1.00 #> log_lik[19] -2.3e-01 1.2e-03 0.077 -0.37 -2.2e-01 -1.2e-01 4012 8761 1.00 #> log_lik[20] -1.1e-01 1.2e-03 0.079 -0.27 -9.4e-02 -2.7e-02 4074 8896 1.00 #> log_lik[21] -2.1e-01 1.4e-03 0.088 -0.37 -2.0e-01 -9.2e-02 3715 8110 1.0 #> log_lik[22] -5.7e-01 2.3e-03 0.15 -0.83 -5.5e-01 -3.5e-01 4001 8736 1.0 #> log_lik[23] -3.3e-01 2.3e-03 0.14 -0.59 -3.1e-01 -1.4e-01 3755 8198 1.00 #> log_lik[24] -1.4e-01 1.1e-03 0.068 -0.26 -1.2e-01 -5.2e-02 3965 8657 1.00 #> log_lik[25] -4.6e-01 1.8e-03 0.12 -0.67 -4.5e-01 -2.8e-01 4284 9354 1.00 #> log_lik[26] -1.5e+00 5.6e-03 0.35 -2.1 -1.5e+00 -9.9e-01 4011 8759 1.00 #> log_lik[27] -3.1e-01 2.0e-03 0.12 -0.53 -2.9e-01 -1.4e-01 3766 8224 1.0 #> log_lik[28] -4.4e-01 1.3e-03 0.085 -0.59 -4.4e-01 -3.1e-01 4028 8795 1.00 #> log_lik[29] -7.3e-01 3.4e-03 0.23 -1.1 -7.1e-01 -4.0e-01 4634 10119 1.00 #> log_lik[30] -7.0e-01 3.1e-03 0.20 -1.0 -6.8e-01 -4.1e-01 3998 8729 1.00 #> log_lik[31] -4.9e-01 2.6e-03 0.16 -0.78 -4.7e-01 -2.6e-01 4003 8741 1.0 #> log_lik[32] -4.2e-01 1.6e-03 0.11 -0.61 -4.1e-01 -2.6e-01 4299 9385 1.0 #> log_lik[33] -4.1e-01 1.9e-03 0.13 -0.63 -4.0e-01 -2.3e-01 4377 9558 1.00 #> log_lik[34] -6.4e-02 8.5e-04 0.052 -0.16 -5.0e-02 -1.3e-02 3746 8179 1.00 #> log_lik[35] -5.9e-01 2.6e-03 0.18 -0.91 -5.7e-01 -3.3e-01 4964 10838 1.00 #> log_lik[36] -3.3e-01 2.1e-03 0.13 -0.58 -3.1e-01 -1.4e-01 4081 8911 1.00 #> log_lik[37] -6.9e-01 3.3e-03 0.23 -1.1 -6.7e-01 -3.7e-01 4588 10017 1.00 #> log_lik[38] -3.2e-01 2.3e-03 0.15 -0.59 -2.9e-01 -1.2e-01 4002 8738 1.00 #> log_lik[39] -1.8e-01 1.7e-03 0.11 -0.39 -1.6e-01 -4.9e-02 4239 9255 1.00 #> log_lik[40] -6.8e-01 1.9e-03 0.13 -0.90 -6.7e-01 -4.9e-01 4339 9474 1.00 #> log_lik[41] -1.1e+00 4.2e-03 0.25 -1.6 -1.1e+00 -7.6e-01 3742 8171 1.0 #> log_lik[42] -9.3e-01 3.0e-03 0.20 -1.3 -9.1e-01 -6.4e-01 4374 9549 1.00 #> log_lik[43] -4.1e-01 3.8e-03 0.27 -0.92 -3.5e-01 -1.0e-01 4940 10786 1.00 #> log_lik[44] -1.2e+00 3.0e-03 0.19 -1.5 -1.2e+00 -8.9e-01 4045 8831 1.00 #> log_lik[45] -3.6e-01 1.9e-03 0.12 -0.58 -3.5e-01 -1.8e-01 4315 9421 1.00 #> log_lik[46] -5.8e-01 1.9e-03 0.13 -0.81 -5.8e-01 -3.9e-01 4621 10089 1.00 #> log_lik[47] -3.1e-01 2.0e-03 0.13 -0.54 -2.9e-01 -1.4e-01 4005 8745 1.00 #> log_lik[48] -3.2e-01 1.3e-03 0.085 -0.48 -3.2e-01 -2.0e-01 4261 9303 1.00 #> log_lik[49] -3.2e-01 1.3e-03 0.080 -0.46 -3.1e-01 -2.0e-01 3930 8581 1.00 #> log_lik[50] -1.3e+00 5.2e-03 0.34 -1.9 -1.3e+00 -7.9e-01 4358 9516 1.00 #> log_lik[51] -2.9e-01 1.4e-03 0.097 -0.47 -2.8e-01 -1.5e-01 4624 10096 1.00 #> log_lik[52] -8.4e-01 2.2e-03 0.15 -1.1 -8.3e-01 -6.1e-01 4377 9558 1.00 #> log_lik[53] -4.0e-01 2.1e-03 0.13 -0.63 -3.9e-01 -2.1e-01 3841 8387 1.0 #> log_lik[54] -3.7e-01 2.2e-03 0.15 -0.63 -3.5e-01 -1.7e-01 4317 9426 1.00 #> log_lik[55] -3.9e-01 2.0e-03 0.13 -0.63 -3.7e-01 -1.9e-01 4429 9671 1.00 #> log_lik[56] -3.2e-01 3.0e-03 0.19 -0.70 -2.8e-01 -9.1e-02 4073 8894 1.00 #> log_lik[57] -6.5e-01 1.7e-03 0.12 -0.86 -6.5e-01 -4.7e-01 4496 9816 1.00 #> log_lik[58] -9.4e-01 4.9e-03 0.35 -1.6 -9.0e-01 -4.5e-01 4920 10743 1.00 #> log_lik[59] -1.4e+00 5.3e-03 0.34 -2.0 -1.3e+00 -8.6e-01 4125 9007 1.00 #> log_lik[60] -9.8e-01 2.5e-03 0.16 -1.3 -9.7e-01 -7.3e-01 4281 9348 1.00 #> log_lik[61] -5.4e-01 1.5e-03 0.10 -0.72 -5.3e-01 -3.9e-01 4572 9982 1.00 #> log_lik[62] -8.8e-01 4.9e-03 0.32 -1.5 -8.5e-01 -4.2e-01 4308 9407 1.0 #> log_lik[63] -1.2e-01 1.2e-03 0.074 -0.26 -1.0e-01 -3.2e-02 3584 7826 1.00 #> log_lik[64] -9.0e-01 4.0e-03 0.25 -1.4 -8.7e-01 -5.4e-01 4099 8950 1.00 #> log_lik[65] -2.0e+00 9.8e-03 0.59 -3.1 -2.0e+00 -1.1e+00 3642 7952 1.0 #> log_lik[66] -5.0e-01 1.9e-03 0.13 -0.74 -4.9e-01 -3.1e-01 4752 10376 1.00 #> log_lik[67] -2.8e-01 1.3e-03 0.083 -0.43 -2.7e-01 -1.6e-01 4034 8808 1.00 #> log_lik[68] -1.1e+00 3.9e-03 0.24 -1.5 -1.0e+00 -7.1e-01 3761 8211 1.00 #> log_lik[69] -4.3e-01 1.3e-03 0.084 -0.58 -4.3e-01 -3.1e-01 4219 9213 1.00 #> log_lik[70] -6.4e-01 3.7e-03 0.24 -1.1 -6.1e-01 -3.0e-01 4278 9341 1.00 #> log_lik[71] -6.1e-01 2.9e-03 0.20 -0.98 -5.9e-01 -3.2e-01 4865 10623 1.0 #> log_lik[72] -4.6e-01 2.5e-03 0.17 -0.76 -4.4e-01 -2.2e-01 4453 9724 1.00 #> log_lik[73] -1.5e+00 5.7e-03 0.36 -2.1 -1.4e+00 -9.3e-01 3935 8591 1.00 #> log_lik[74] -9.5e-01 3.0e-03 0.20 -1.3 -9.4e-01 -6.6e-01 4389 9583 1.00 #> log_lik[75] -1.1e+00 6.1e-03 0.40 -1.9 -1.1e+00 -5.7e-01 4353 9505 1.0 #> log_lik[76] -3.7e-01 2.2e-03 0.14 -0.62 -3.5e-01 -1.7e-01 4299 9387 1.00 #> log_lik[77] -8.8e-01 2.1e-03 0.14 -1.1 -8.7e-01 -6.7e-01 4303 9396 1.0 #> log_lik[78] -4.9e-01 2.6e-03 0.18 -0.82 -4.6e-01 -2.4e-01 4716 10297 1.00 #> log_lik[79] -7.6e-01 2.9e-03 0.19 -1.1 -7.5e-01 -4.8e-01 4325 9444 1.00 #> log_lik[80] -5.4e-01 2.9e-03 0.20 -0.91 -5.2e-01 -2.6e-01 4653 10160 1.00 #> log_lik[81] -1.6e-01 1.6e-03 0.099 -0.35 -1.4e-01 -4.9e-02 3852 8410 1.00 #> log_lik[82] -2.2e-01 2.1e-03 0.14 -0.49 -1.9e-01 -6.1e-02 4220 9215 1.00 #> log_lik[83] -3.4e-01 1.3e-03 0.083 -0.49 -3.4e-01 -2.2e-01 4202 9174 1.00 #> log_lik[84] -2.7e-01 1.4e-03 0.092 -0.44 -2.6e-01 -1.4e-01 4250 9280 1.00 #> log_lik[85] -1.3e-01 1.2e-03 0.075 -0.27 -1.1e-01 -4.0e-02 4072 8891 1.00 #> log_lik[86] -1.1e+00 5.0e-03 0.32 -1.7 -1.1e+00 -6.5e-01 4140 9040 1.00 #> log_lik[87] -8.3e-01 2.0e-03 0.13 -1.0 -8.2e-01 -6.3e-01 4293 9373 1.00 #> log_lik[88] -7.8e-01 3.5e-03 0.24 -1.2 -7.5e-01 -4.3e-01 4503 9832 1.0 #> log_lik[89] -1.3e+00 4.9e-03 0.32 -1.9 -1.2e+00 -8.1e-01 4104 8960 1.00 #> log_lik[90] -2.6e-01 2.1e-03 0.13 -0.52 -2.4e-01 -9.4e-02 4118 8991 1.00 #> log_lik[91] -3.9e-01 1.9e-03 0.13 -0.61 -3.7e-01 -2.1e-01 4368 9537 1.00 #> log_lik[92] -1.5e+00 5.4e-03 0.34 -2.1 -1.5e+00 -9.8e-01 4061 8866 1.00 #> log_lik[93] -7.5e-01 3.6e-03 0.23 -1.2 -7.2e-01 -4.2e-01 4046 8835 1.00 #> log_lik[94] -3.2e-01 1.4e-03 0.089 -0.47 -3.1e-01 -1.9e-01 4234 9244 1.00 #> log_lik[95] -3.9e-01 1.8e-03 0.11 -0.58 -3.8e-01 -2.2e-01 3790 8276 1.0 #> log_lik[96] -1.6e+00 4.8e-03 0.29 -2.1 -1.6e+00 -1.1e+00 3777 8248 1.00 #> log_lik[97] -4.3e-01 1.6e-03 0.10 -0.62 -4.2e-01 -2.7e-01 4262 9306 1.00 #> log_lik[98] -1.0e+00 5.2e-03 0.36 -1.7 -1.0e+00 -5.2e-01 4933 10771 1.00 #> log_lik[99] -6.9e-01 2.1e-03 0.14 -0.94 -6.9e-01 -4.8e-01 4361 9523 1.00 #> log_lik[100] -3.9e-01 1.5e-03 0.10 -0.57 -3.8e-01 -2.4e-01 4557 9949 1.00 #> #> 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).# }