This function takes in the output from a cmdstanr$sample() function (the fit object) and a series of diagnostic toleraances and returns a dataframe containing flags for whether any of the diagnostic thresholds were exceeded, which would indicate that the model did not properly converge
Usage
get_diagnostic_flags(
stan_fit_object,
n_chains,
iter_sampling,
ebmfi_tolerance = 0.2,
divergences_tolerance = 0.01,
p_high_rhat_tolerance = 0.05,
max_tree_depth_tol = 0.01
)Arguments
- stan_fit_object
The R6 Cmdstan Object fit object
- n_chains
number of chains fun
- iter_sampling
number of sampling iterations
- ebmfi_tolerance
Tolerance for EBMFI (bayesian missing information)
- divergences_tolerance
tolerance for proportion of sampling iterations that are divergent
- p_high_rhat_tolerance
tolerance for proportion of parameters rhats>1.05
- max_tree_depth_tol
tolerance for proportion of iterations that exceed the maximum tree depth