Extract and return the model summary using cmdstanr::summary().
Arguments
- model_output
List. Model output generated by
run_model().- variables
Character vector. Specific variables (e.g.,
"strata_raw[1]") or variable types (e.g.,"strata_raw") for which to calculate metrics. IfNULL(default) all variables are returned.
Value
A data frame of model summary statistics, matching the output of
cmdstanr::summary() plus one additional column variable_type that
identifies categories of parameters (e.g., n for all of the annual
indices for every stratum and year).
See also
Other model assessment functions:
get_convergence(),
get_model_vars()
Examples
# Temporarily suppress convergence warning for legibility
# "The ESS has been capped to avoid unstable estimates."
opts <- options(warn = -1)
# Using the example model for Pacific Wrens
get_summary(pacific_wren_model)
#> # A tibble: 11,150 × 11
#> variable_type variable mean median sd mad q5 q95
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 lp__ lp__ -1.47e+4 -1.47e+4 43.3 49.4 -1.47e+4 -1.46e+4
#> 2 strata_raw strata_raw[1] -8.78e-1 -9.08e-1 0.416 0.357 -1.42e+0 -2.68e-1
#> 3 strata_raw strata_raw[2] -1.62e-1 -1.79e-1 0.181 0.163 -5.34e-1 1.05e-1
#> 4 strata_raw strata_raw[3] -2.19e-1 -2.27e-1 0.516 0.486 -1.20e+0 4.65e-1
#> 5 strata_raw strata_raw[4] 1.51e+0 1.57e+0 0.280 0.268 1.03e+0 1.86e+0
#> 6 strata_raw strata_raw[5] -2.35e-1 -2.31e-1 0.251 0.258 -6.48e-1 1.73e-1
#> 7 strata_raw strata_raw[6] 1.17e+0 1.15e+0 0.489 0.463 3.51e-1 1.97e+0
#> 8 strata_raw strata_raw[7] -1.10e+0 -1.06e+0 0.478 0.585 -1.75e+0 -3.99e-1
#> 9 strata_raw strata_raw[8] 1.87e+0 1.82e+0 0.406 0.391 1.24e+0 2.41e+0
#> 10 strata_raw strata_raw[9] -9.28e-1 -9.52e-1 0.349 0.364 -1.41e+0 -4.19e-1
#> # ℹ 11,140 more rows
#> # ℹ 3 more variables: rhat <dbl>, ess_bulk <dbl>, ess_tail <dbl>
get_summary(pacific_wren_model, variables = "strata_raw")
#> # A tibble: 19 × 11
#> variable_type variable mean median sd mad q5 q95 rhat
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 strata_raw strata_raw[1] -0.878 -0.908 0.416 0.357 -1.42 -0.268 1.03
#> 2 strata_raw strata_raw[2] -0.162 -0.179 0.181 0.163 -0.534 0.105 0.999
#> 3 strata_raw strata_raw[3] -0.219 -0.227 0.516 0.486 -1.20 0.465 1.03
#> 4 strata_raw strata_raw[4] 1.51 1.57 0.280 0.268 1.03 1.86 1.02
#> 5 strata_raw strata_raw[5] -0.235 -0.231 0.251 0.258 -0.648 0.173 1.05
#> 6 strata_raw strata_raw[6] 1.17 1.15 0.489 0.463 0.351 1.97 0.970
#> 7 strata_raw strata_raw[7] -1.10 -1.06 0.478 0.585 -1.75 -0.399 1.06
#> 8 strata_raw strata_raw[8] 1.87 1.82 0.406 0.391 1.24 2.41 1.09
#> 9 strata_raw strata_raw[9] -0.928 -0.952 0.349 0.364 -1.41 -0.419 0.997
#> 10 strata_raw strata_raw[10] -0.442 -0.465 0.329 0.209 -1.10 0.0573 0.980
#> 11 strata_raw strata_raw[11] -0.298 -0.325 0.251 0.241 -0.672 0.0890 1.02
#> 12 strata_raw strata_raw[12] 0.425 0.428 0.304 0.267 0.0362 1.01 1.14
#> 13 strata_raw strata_raw[13] -0.667 -0.653 0.337 0.341 -1.20 -0.147 1.01
#> 14 strata_raw strata_raw[14] -1.07 -1.06 0.365 0.318 -1.72 -0.441 1.15
#> 15 strata_raw strata_raw[15] 0.623 0.643 0.174 0.182 0.369 0.830 1.01
#> 16 strata_raw strata_raw[16] -0.845 -0.763 0.541 0.500 -1.87 -0.285 1.02
#> 17 strata_raw strata_raw[17] -0.578 -0.547 0.385 0.388 -1.15 -0.0237 1.01
#> 18 strata_raw strata_raw[18] 1.25 1.20 0.310 0.246 0.816 1.75 1.25
#> 19 strata_raw strata_raw[19] 0.559 0.587 0.270 0.264 0.180 0.946 1.06
#> # ℹ 2 more variables: ess_bulk <dbl>, ess_tail <dbl>
get_summary(pacific_wren_model, variables = "strata_raw[9]")
#> # A tibble: 1 × 11
#> variable_type variable mean median sd mad q5 q95 rhat ess_bulk
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 strata_raw strata_ra… -0.928 -0.952 0.349 0.364 -1.41 -0.419 0.997 58.6
#> # ℹ 1 more variable: ess_tail <dbl>
# Restore warnings
options(opts)