Format data for data-augmented occupancy model, to be passed to flock().

Source: R/make_flocker_data.R

Format data for data-augmented occupancy model, to be passed to flock().

make_flocker_data_augmented(
  obs,
  n_aug,
  site_covs = NULL,
  event_covs = NULL,
  quiet = FALSE,
  newdata_checks = FALSE
)

Arguments

obs

An I x J x K array where rows I are sites, columns J are repeat sampling events, and slices K are species. Allowable values are 1 (detection), 0 (no detection), and NA (no sampling event). Every supplied species must have at least one detection; never-observed pseudospecies are added through n_aug. Species names may be supplied as names on the third dimension. If omitted, observed species are named `species1`, `species2`, and so on. Names matching `pseudospecies[digits]` are reserved for augmented pseudospecies. The data must be formatted so that all NAs are trailing within their rows.

n_aug

Number of pseudospecies to augment

site_covs

A dataframe of covariates for each site that are constant across repeated sampling events.

event_covs

A named list of I x J matrices, each one corresponding to a covariate that varies across repeated sampling events within sites

quiet

Hide progress bars and informational messages?

newdata_checks

If TRUE, turn off checks that must pass in order to use the data for model fitting, but not in other contexts (e.g. making predictions or assessing log-likelihoods over new data).

Value

A flocker_data list that can be passed as data to flocker().