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: 10,917 × 5
#> variable_type variable rhat ess_bulk ess_tail
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 lp__ lp__ 1.00 26.9 21.0
#> 2 strata_raw strata_raw[1] 1.03 64.1 49.6
#> 3 strata_raw strata_raw[2] 1.00 64.1 49.6
#> 4 strata_raw strata_raw[3] 0.966 64.1 43.9
#> 5 strata_raw strata_raw[4] 0.981 56.4 28.0
#> 6 strata_raw strata_raw[5] 1.01 52.3 37.7
#> 7 strata_raw strata_raw[6] 1.24 64.1 18.9
#> 8 strata_raw strata_raw[7] 1.01 30.7 22.4
#> 9 strata_raw strata_raw[8] 1.03 54.7 28.0
#> 10 strata_raw strata_raw[9] 0.987 64.1 43.9
#> # ℹ 10,907 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 64.1 49.6
#> 2 strata_raw strata_raw[2] 1.00 64.1 49.6
#> 3 strata_raw strata_raw[3] 0.966 64.1 43.9
#> 4 strata_raw strata_raw[4] 0.981 56.4 28.0
#> 5 strata_raw strata_raw[5] 1.01 52.3 37.7
#> 6 strata_raw strata_raw[6] 1.24 64.1 18.9
#> 7 strata_raw strata_raw[7] 1.01 30.7 22.4
#> 8 strata_raw strata_raw[8] 1.03 54.7 28.0
#> 9 strata_raw strata_raw[9] 0.987 64.1 43.9
#> 10 strata_raw strata_raw[10] 1.10 64.1 56.9
#> 11 strata_raw strata_raw[11] 0.966 62.5 22.4
#> 12 strata_raw strata_raw[12] 1.02 64.1 21.4
#> 13 strata_raw strata_raw[13] 0.983 64.1 30.7
#> 14 strata_raw strata_raw[14] 1.04 64.1 23.5
#> 15 strata_raw strata_raw[15] 1.07 64.1 49.6
#> 16 strata_raw strata_raw[16] 1.06 64.1 37.7
#> 17 strata_raw strata_raw[17] 0.999 64.1 49.6
#> 18 strata_raw strata_raw[18] 0.999 51.9 28.0
#> 19 strata_raw strata_raw[19] 1.07 64.1 49.6
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] 0.987 64.1 43.9
# Restore warnings
options(opts)