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: 10,495 × 5
#> variable_type variable rhat ess_bulk ess_tail
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 lp__ lp__ 1.04 25.7 49.6
#> 2 strata_raw strata_raw[1] 1.01 61.6 37.7
#> 3 strata_raw strata_raw[2] 0.985 29.4 49.6
#> 4 strata_raw strata_raw[3] 1.02 35.8 49.6
#> 5 strata_raw strata_raw[4] 1.15 50.6 56.9
#> 6 strata_raw strata_raw[5] 1.03 30.0 56.9
#> 7 strata_raw strata_raw[6] 1.07 31.6 22.4
#> 8 strata_raw strata_raw[7] 0.992 36.2 49.6
#> 9 strata_raw strata_raw[8] 1.04 28.4 49.6
#> 10 strata_raw strata_raw[9] 0.973 53.0 17.3
#> # ℹ 10,485 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] 1.01 61.6 37.7
#> 2 strata_raw strata_raw[2] 0.985 29.4 49.6
#> 3 strata_raw strata_raw[3] 1.02 35.8 49.6
#> 4 strata_raw strata_raw[4] 1.15 50.6 56.9
#> 5 strata_raw strata_raw[5] 1.03 30.0 56.9
#> 6 strata_raw strata_raw[6] 1.07 31.6 22.4
#> 7 strata_raw strata_raw[7] 0.992 36.2 49.6
#> 8 strata_raw strata_raw[8] 1.04 28.4 49.6
#> 9 strata_raw strata_raw[9] 0.973 53.0 17.3
#> 10 strata_raw strata_raw[10] 0.970 64.1 56.9
#> 11 strata_raw strata_raw[11] 1.07 25.2 56.9
#> 12 strata_raw strata_raw[12] 0.994 64.1 56.9
#> 13 strata_raw strata_raw[13] 1.02 46.5 18.9
#> 14 strata_raw strata_raw[14] 1.11 64.1 49.6
#> 15 strata_raw strata_raw[15] 0.996 64.1 36.3
#> 16 strata_raw strata_raw[16] 0.999 57.1 56.9
#> 17 strata_raw strata_raw[17] 0.997 34.2 23.5
#> 18 strata_raw strata_raw[18] 1.04 39.1 17.3
#> 19 strata_raw strata_raw[19] 1.05 26.5 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] 0.973 53.0 17.3
# Restore warnings
options(opts)