Calculate convergence metrics for the model run. Specifically calculates bulk
and tail effective sample sizes (ess_bulk, ess_tail) and R-hat (rhat).
Returns output very similar to get_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
Data frame of convergence metrics for all model variables. Contains
variable_type, variable, ess_bulk, ess_tail, and rhat.
See also
Other model assessment functions:
get_model_vars(),
get_summary()
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_convergence(pacific_wren_model)
#> # A tibble: 11,150 × 5
#> variable_type variable rhat ess_bulk ess_tail
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 lp__ lp__ 0.966 52.4 56.9
#> 2 strata_raw strata_raw[1] 1.03 35.3 40.7
#> 3 strata_raw strata_raw[2] 0.999 64.1 49.6
#> 4 strata_raw strata_raw[3] 1.03 34.0 56.9
#> 5 strata_raw strata_raw[4] 1.02 38.0 49.6
#> 6 strata_raw strata_raw[5] 1.05 30.3 17.3
#> 7 strata_raw strata_raw[6] 0.970 64.1 56.9
#> 8 strata_raw strata_raw[7] 1.06 39.3 56.9
#> 9 strata_raw strata_raw[8] 1.09 17.7 24.6
#> 10 strata_raw strata_raw[9] 0.997 58.6 56.9
#> # ℹ 11,140 more rows
get_convergence(pacific_wren_model, variables = "strata_raw")
#> # A tibble: 19 × 5
#> variable_type variable rhat ess_bulk ess_tail
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 strata_raw strata_raw[1] 1.03 35.3 40.7
#> 2 strata_raw strata_raw[2] 0.999 64.1 49.6
#> 3 strata_raw strata_raw[3] 1.03 34.0 56.9
#> 4 strata_raw strata_raw[4] 1.02 38.0 49.6
#> 5 strata_raw strata_raw[5] 1.05 30.3 17.3
#> 6 strata_raw strata_raw[6] 0.970 64.1 56.9
#> 7 strata_raw strata_raw[7] 1.06 39.3 56.9
#> 8 strata_raw strata_raw[8] 1.09 17.7 24.6
#> 9 strata_raw strata_raw[9] 0.997 58.6 56.9
#> 10 strata_raw strata_raw[10] 0.980 63.9 49.6
#> 11 strata_raw strata_raw[11] 1.02 36.1 21.0
#> 12 strata_raw strata_raw[12] 1.14 20.5 22.4
#> 13 strata_raw strata_raw[13] 1.01 50.6 43.9
#> 14 strata_raw strata_raw[14] 1.15 15.1 51.1
#> 15 strata_raw strata_raw[15] 1.01 41.8 32.6
#> 16 strata_raw strata_raw[16] 1.02 58.1 21.4
#> 17 strata_raw strata_raw[17] 1.01 51.2 49.6
#> 18 strata_raw strata_raw[18] 1.25 8.90 17.3
#> 19 strata_raw strata_raw[19] 1.06 26.2 21.4
get_convergence(pacific_wren_model, variables = "strata_raw[9]")
#> # A tibble: 1 × 5
#> variable_type variable rhat ess_bulk ess_tail
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 strata_raw strata_raw[9] 0.997 58.6 56.9
# Restore warnings
options(opts)