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: 10,917 × 11
#> variable_type variable mean median sd mad q5 q95
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 lp__ lp__ -1.44e+4 -1.44e+4 36.0 33.6 -1.45e+4 -1.44e+4
#> 2 strata_raw strata_raw[1] -9.51e-1 -9.96e-1 0.514 0.625 -1.71e+0 -1.67e-1
#> 3 strata_raw strata_raw[2] -2.70e-1 -2.49e-1 0.231 0.162 -6.31e-1 4.68e-2
#> 4 strata_raw strata_raw[3] -1.33e-1 -1.86e-1 0.570 0.605 -9.74e-1 7.05e-1
#> 5 strata_raw strata_raw[4] 1.53e+0 1.57e+0 0.279 0.266 1.08e+0 2.03e+0
#> 6 strata_raw strata_raw[5] -2.25e-1 -1.75e-1 0.260 0.216 -5.83e-1 1.38e-1
#> 7 strata_raw strata_raw[6] 1.24e+0 1.27e+0 0.607 0.647 2.96e-1 2.04e+0
#> 8 strata_raw strata_raw[7] -9.12e-1 -9.86e-1 0.485 0.448 -1.49e+0 -1.33e-1
#> 9 strata_raw strata_raw[8] 1.82e+0 1.82e+0 0.390 0.387 1.27e+0 2.42e+0
#> 10 strata_raw strata_raw[9] -9.54e-1 -8.51e-1 0.334 0.301 -1.51e+0 -5.56e-1
#> # ℹ 10,907 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] -0.951 -0.996 0.514 0.625 -1.71 -0.167 1.03
#> 2 strata_raw strata_raw[2] -0.270 -0.249 0.231 0.162 -0.631 0.0468 1.00
#> 3 strata_raw strata_raw[3] -0.133 -0.186 0.570 0.605 -0.974 0.705 0.966
#> 4 strata_raw strata_raw[4] 1.53 1.57 0.279 0.266 1.08 2.03 0.981
#> 5 strata_raw strata_raw[5] -0.225 -0.175 0.260 0.216 -0.583 0.138 1.01
#> 6 strata_raw strata_raw[6] 1.24 1.27 0.607 0.647 0.296 2.04 1.24
#> 7 strata_raw strata_raw[7] -0.912 -0.986 0.485 0.448 -1.49 -0.133 1.01
#> 8 strata_raw strata_raw[8] 1.82 1.82 0.390 0.387 1.27 2.42 1.03
#> 9 strata_raw strata_raw[9] -0.954 -0.851 0.334 0.301 -1.51 -0.556 0.987
#> 10 strata_raw strata_raw[10] -0.414 -0.423 0.388 0.333 -1.15 0.204 1.10
#> 11 strata_raw strata_raw[11] -0.241 -0.200 0.253 0.220 -0.786 0.0617 0.966
#> 12 strata_raw strata_raw[12] 0.358 0.336 0.242 0.207 0.0146 0.680 1.02
#> 13 strata_raw strata_raw[13] -0.673 -0.605 0.329 0.255 -1.10 -0.196 0.983
#> 14 strata_raw strata_raw[14] -0.966 -0.932 0.336 0.323 -1.48 -0.486 1.04
#> 15 strata_raw strata_raw[15] 0.639 0.672 0.240 0.302 0.289 0.967 1.07
#> 16 strata_raw strata_raw[16] -0.822 -0.808 0.456 0.385 -1.45 -0.210 1.06
#> 17 strata_raw strata_raw[17] -0.689 -0.614 0.395 0.274 -1.27 -0.224 0.999
#> 18 strata_raw strata_raw[18] 1.19 1.19 0.358 0.203 0.752 1.71 0.999
#> 19 strata_raw strata_raw[19] 0.478 0.489 0.330 0.317 -0.0779 1.01 1.07
#> # 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… -0.954 -0.851 0.334 0.301 -1.51 -0.556 0.987 64.1
#> # ℹ 1 more variable: ess_tail <dbl>
# Restore warnings
options(opts)