R: Simulate data for use with 'make_flocker

simulate_flocker_data {flocker}

R Documentation

Simulate data for use with `make_flocker_data()` and downstream functions.

Description

Data will be simulated with one unit covariate that affects all relevant terms, one event covariate that affects detection (unless 'rep_constant' is 'TRUE'), and one grouping factor representing species with correlated effects on all terms.

Usage

simulate_flocker_data(
  n_rep = 4,
  n_pt = 50,
  n_sp = 30,
  n_season = 1,
  multiseason = NULL,
  multi_init = NULL,
  augmented = FALSE,
  rep_constant = FALSE,
  params = NULL,
  covariates = NULL,
  seed = 123,
  ragged_rep = FALSE,
  missing_seasons = FALSE
)

Arguments

`n_rep`	number of replicate visits to simulate per closure unit
`n_pt`	number of points to simulate. The number of units for single- season models will be 'n_ptn_sp'. The number of units for multi-season models will be 'n_ptn_sp*n_season'.
`n_sp`	number of levels to include in random effect. For compatibility with multispecies models where the random effect represents species, the data get expanded such that there's a row (closure-unit) for each combination of sampling point and effect level (i.e. species)
`n_season`	Number of seasons desired. 1 yields data for a single-season model; all other positive integers yield data for multiseason models.
`multiseason`	if n_season is NULL, must be NULL. Otherwise, one of "colex" or "autologistic".
`multi_init`	if n_season is NULL, must be NULL. Otherwise, one of "explicit" or "equilibrium".
`augmented`	logical. If 'TRUE' data will be formatted for an augmented model, which requires that 'n_season == 1'. All never-observed species will be trimmed out of the data, and the default parameters will be modified to increase random effect variances for the detection and occupancy, intercepts and to decrease random effect variances for detection slopes, thus encouraging the existence of never-observed species. Furthermore, the data will be simulated without any covariate influence on occupancy.
`rep_constant`	logical: create data with unit covariates only (TRUE) or data that includes event covariates (FALSE)
`params`	a named list containing of parameter values to use in simulation. Any required parameters whose names are not in this list will be assigned their default values. To see the parameter names and structures required, run with 'params = NULL' (the default) and examine the '$params' element of the output.
`covariates`	a dataframe of covariate values to use in simulation, or NULL to simulate values. To see the covariate names and structures required, run with 'covariates = NULL' (the default) and examine the '$covariates' element of the output.
`seed`	random seed. NULL uses (and updates) the existing RNG state. Other values do not update the global RNG state.
`ragged_rep`	logical: create data with variable (TRUE) or constant (FALSE) numbers of visits per unit. If TRUE, approximately half of units will be missing approximately half of 'n_rep' visits. Intended primarily for development purposes (bug-checking models with missing data).
`missing_seasons`	logical; relevant only if n_season is greater than 1. create data with variable (TRUE) or constant (FALSE) numbers of seasons per series (TRUE). If TRUE, approximately half of series will be missing their even-numbered seasons.

Value

A named list with the observation matrix/array ($obs), the unit covariate dataframe(s) ($unit_covs), the event covariate list ($event_covs), the parameters used in simulation ($params) and the covariate list used in simulation ($covariates). If rep_constant is TRUE, then $event_covs will be NULL.

Examples

simulate_flocker_data()