summary.jsdmStanFit: Summarise the model fit and data structure and give summaries...

In fseaton/jsdmstan: Fitting jSDMs in Stan

Summarise the model fit and data structure and give summaries for the parameters

Description

This returns a matrix of parameter summaries including a summary of the parameter estimates, R-hat, bulk ESS and tail ESS. This can be limited to parameters with Rhat > 1.01 or ESS < 500 by setting prob_pars_only = TRUE.

Usage

## S3 method for class 'jsdmStanFit'
summary(
  object,
  prob_quantiles = c(0.15, 0.85),
  digit_summary = 3,
  prob_pars_only = FALSE,
  pars = NULL,
  na_filter = TRUE,
  log_lik = FALSE,
  ...
)

Arguments

object	The model object
prob_quantiles	The quantiles to summarise the parameter estimates with, by default the 15% and 85% quantiles
digit_summary	The number of digits to round the results to
prob_pars_only	Whether to limit output to parameters with Rhat > 1.01 or effective sample size < 500, by default FALSE
pars	Parameters to compute the summary of, by default NULL i.e. all parameters included
na_filter	Whether to remove parameters with NAs in Rhat - this includes the parameters fixed to zero or one, such as the upper triangle of the cholesky factor of the correlation matrix. By default TRUE
log_lik	Whether the log_lik parameters should be included, default FALSE
...	Arguments passed to extract()

Examples

## Not run: 

gllvm_data <- jsdm_sim_data(
  method = "gllvm", N = 100, S = 6, D = 2,
  family = "bernoulli"
)
gllvm_fit <- stan_jsdm(
  dat_list = gllvm_data, method = "gllvm",
  family = "bernoulli"
)
gllvm_summ <- summary(gllvm_fit)
head(gllvm_summ, 20)

summary(gllvm_fit, prob_quantiles = c(0.05, 0.5, 0.95))

## End(Not run)

fseaton/jsdmstan documentation built on Sept. 29, 2024, 6:40 p.m.