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Draw from the posterior predictive distribution

posterior_predict.jsdmStanFit.Rd

Draw from the posterior predictive distribution of the outcome.

Usage

# S3 method for class 'jsdmStanFit'
posterior_predict(
  object,
  newdata = NULL,
  ndraws = NULL,
  draw_ids = NULL,
  list_index = "draws",
  Ntrials = NULL,
  include_zi = TRUE,
  include_shp = TRUE,
  zi_newdata = NULL,
  shp_newdata = NULL,
  ...
)

Arguments

object

The model object

newdata

New data, by default NULL and uses original data

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.

draw_ids

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

list_index

Whether to return the output list indexed by the number of draws (default), species, or site.

Ntrials

For the binomial distribution the number of trials, given as either a single integer which is assumed to be constant across sites or as a site-length vector of integers.

include_zi

For the zero-inflated distributions, whether to include the zero-inflation in the prediction. Defaults to TRUE.

include_shp

For the distributions where the shape parameter is responsive to environmental predictors, whether to include this effect in the prediction. Defaults to TRUE.

zi_newdata

For the zero-inflated distributions, the data used to fit any parameter effect upon the zi parameter. Defaults to NULL and uses original data.

shp_newdata

For the distributions where the shape parameter is responsive to environmental predictors, any updated data for this effect in the prediction. Defaults to NULL and uses original data.

...

Currently unused

Value

A list of linear predictors. If list_index is "draws" (the default) the list will have length equal to the number of draws with each element of the list being a site x species matrix. If the list_index is "species" the list will have length equal to the number of species with each element of the list being a draws x sites matrix. If the list_index is "sites" the list will have length equal to the number of sites with each element of the list being a draws x species matrix.

See also

posterior_linpred.jsdmStanFit()