make_flocker_data: Format data for occupancy model with 'flock()'.

In jsocolar/flocker: Flexible Occupancy Estimation with Stan

Format data for occupancy model with flock().

Description

Format data for occupancy model with flock().

Usage

make_flocker_data(
  obs,
  unit_covs = NULL,
  event_covs = NULL,
  type = "single",
  n_aug = NULL,
  quiet = FALSE,
  newdata_checks = FALSE
)

Arguments

obs	If type = "single", an I x J matrix-like object where closure is assumed across rows and columns are repeated sampling events. If type = "multi", an I x J x K array where rows are sites or species-sites, columns are repeated sampling events, and slices along the third dimension are seasons. Allowable values are 1 (detection), 0 (no detection), and NA (no sampling event). If type = "augmented", an L x J x K array where rows L are sites, columns J are repeat sampling events, and slices K are species. The data must be packed so that, for a given unit (site, site-species, site-timestep, site-species-timestep) all realized visits come before any missing visits (NAs are trailing within their rows).
unit_covs	If type = "single" a dataframe of covariates for each closure-unit that are constant across repeated sampling events within units. If type = "multi", a list of such dataframes, one per timestep. All dataframes must have identical column names and types, and all dataframes must have I rows. If type = "augmented", a dataframe of covariates for each site that are constant across repeated sampling events within sites (no dependence on species is allowed).
event_covs	If type = "single", a named list of I x J matrices, each one corresponding to a covariate that varies across repeated sampling events within closure-units. If type = "multi", a named list of I x J x K arrays, each one corresponding to a covariate that varies across repeated sampling events within closure-units. If type = "augmented", a named list of L x J matrices, each one corresponding to a covariate that varies across repeated sampling events within sites (no dependence on species is allowed).
type	The type of occupancy model desired. Options are: "single" for a single_season model, "multi" for a multi-season (dynamic) model, or "augmented" for a single-season multi-species model with data-augmentation for never-observed pseudospecies.
n_aug	Number of pseudo-species to augment. Only applicable if type = "augmented".
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 flock().

Examples

sfd <- simulate_flocker_data()
make_flocker_data(
 sfd$obs, 
 sfd$unit_covs,
 sfd$event_covs
)

jsocolar/flocker documentation built on Jan. 29, 2025, 11:18 p.m.