get_Z: Get posterior distribution of the Z matrix
In jsocolar/flocker: Flexible Occupancy Estimation with Stan

get_Z

R Documentation

Get posterior distribution of the Z matrix

Description

Get posterior distribution of the Z matrix

Usage

get_Z(
  flocker_fit,
  draw_ids = NULL,
  history_condition = TRUE,
  sample = FALSE,
  new_data = NULL,
  allow_new_levels = FALSE,
  sample_new_levels = "uncertainty"
)

Arguments

`flocker_fit`	A flocker_fit object
`draw_ids`	Vector of indices of the posterior draws to be used. If 'NULL' (the default) all draws are used in their native order.
`history_condition`	Should the posterior distribution for Z directly condition on the observed detection history ('TRUE') or not ('FALSE')? For example, at sites with at least one detection, the true occupancy state conditioned on the history is one with absolute certainty. Without directly conditioning on the history, the occupancy state is controlled by the posterior distribution for the occupancy probability psi.
`sample`	Should the return be posterior probabilities of occupancy (FALSE), or bernoulli samples from those probabilities (TRUE)
`new_data`	Optional new data at which to predict the Z matrix. Can be the output of 'make_flocker_data' or the 'unit_covs' input to 'make_flocker_data' provided that 'history_condition' is 'FALSE' and the occupancy model is a single-season, non-augmented model.
`allow_new_levels`	allow new levels for random effect terms in 'new_data'? Will error if set to 'FALSE' and new levels are provided in 'new_data'.
`sample_new_levels`	If 'new_data' is provided and contains random effect levels not present in the original data, how should predictions be handled? Passed directly to 'brms::prepare_predictions', which see.

Value

The posterior Z matrix in the shape of the first visit in 'obs' as passed to make_flocker_data, with posterior iterations stacked along the final dimension