Extract site- or species-level summary statistics for predictions from a jsdmStanFit model

This function extracts the predicted Y values for within the models and then calculates summary statistics for each simulated community. The default is to sum all the predicted scores for each site.

Usage

jsdm_statsummary(
  object,
  species = NULL,
  sites = NULL,
  summary_stat = "sum",
  post_type = "linpred",
  calc_over = "site",
  simplify = TRUE,
  draw_ids = NULL,
  ndraws = NULL,
  ...
)

Arguments

object

A jsdmStanFit model object

species

Which species to include in the summary statistic, by default all

sites

Which sites to include in the summary statistic, by default all

summary_stat

The summary statistic to be used, by default sum but any function can be used.

post_type

The type of posterior prediction to be used, either "linpred" for posterior_linpred.jsdmStanFit() or "predict" for posterior_predict.jsdmStanFit()

calc_over

Whether to calculate the summary statistic by site or species, by default species

simplify

Whether to simplify the output into a matrix, by default TRUE

draw_ids

The IDs of the draws to be used, as a numeric vector

ndraws

Number of draws, by default the number of samples in the posterior. Will be sampled randomly from the chains if fewer than the number of samples.

...

Arguments passed to the posterior prediction function

Value

If simplify = TRUE then a matrix where each row is a draw and each column is either a site (if calc_over = "site") or a species (if calc_over = "species").

See also

pp_check.jsdmStanFit

Examples

if (FALSE) { # \dontrun{
# First simulate data and fit the jsdmStan model:
gllvm_data <- gllvm_sim_data(
  N = 100, S = 9, D = 2,
  family = "bernoulli"
)
gllvm_fit <- stan_gllvm(dat_list = gllvm_data, family = "bernoulli")

# The default is to return a matrix:
jsdm_statsummary(gllvm_fit)

# The above returns the linear predictor, while we may want to get the posterior
# prediction instead:
jsdm_statsummary(gllvm_fit, post_type = "predict")

# This can be limited to a specific set of species and/or sites:
jsdm_statsummary(gllvm_fit, species = 1:5, sites = seq(5, 95, 10))
} # }