get_flocker_prior {flocker}

Get prior for occupancy model

Description

Get prior for occupancy model

Usage

get_flocker_prior(
  f_occ = NULL,
  f_det,
  flocker_data,
  data2 = NULL,
  multiseason = NULL,
  f_col = NULL,
  f_ex = NULL,
  multi_init = NULL,
  f_auto = NULL,
  augmented = FALSE,
  threads = NULL,
  ...
)

Arguments

f_occ

A brms-type model formula for occupancy. If provided, must begin with "~".

f_det

A brms-type model formula for detection. Must begin with "~". OR, a brmsformula object including formulas for all of the relevant distributional parameters in the desired model (det and at least one of occ, colo, ex, autologistic, and Omega). The $formula element of the brmsformula must be the detection formula, beginning with det ~. This latter option unadvisable except when necessary (e.g. when a nonlinear formula is desired), as input checking is less thorough.

flocker_data

data, generally the output of make_flocker_data().

data2

additional data (e.g. a covariance matrix for a phylogenetic effect)

multiseason

Must be NULL (the default) or one of "colex" or "autologistic". If NULL, data must be formatted for a single-season model. Otherwise, the data must be formatted for a multiseason model. If "colex", a colonization-extinction model will be fit, and 'f_col' and 'f_ex' must be specified. If "autologistic", an autologistic model will be fit, and 'f_col' and 'f_ex' must both be NULL.

f_col

A brms-type model formula for colonization in colonization-extinction dynamic models. If provided, must begin with "~".

f_ex

A brms-type model formula for extinction probabilities in colonization-extinction dynamic models. If provided, must begin with "~".

multi_init

Must be NULL unless the model is a dynamic (multiseason) model, in which case must be either "explicit" or "equilibrium". If "explicit", then 'f_occ' must be provided to model occupancy probabilities in the first timestep. If "equilibrium", then 'f_occ' must be 'NULL' and the initial occupancy probabilities are assumed to be the (possibly site-specific) equilibrium probabilities from the colonization- extinction dynamics.

f_auto

Relevant only for autologistic models. A brms-type model formula for the autologistic offset parameter (theta). If provided, must begin with "~".

augmented

Logical. Must be TRUE if data are formatted for a data-augmented multi-species model, and FALSE otherwise.

threads

NULL or positive integer. If integer, the number of threads to use per chain in within chain parallelization. Currently available only with single-season rep-constant models, and must be set to NULL otherwise.

...

additional arguments passed to brms::brm()

Value

A dataframe summarizing the parameters on which priors can be specified and giving the default priors for those parameters. See ?brms::get_prior for further details.

Examples

sfd <- simulate_flocker_data()
fd <- make_flocker_data(
 sfd$obs, 
 sfd$unit_covs,
 sfd$event_covs
)
get_flocker_prior(
 f_occ = ~ s(uc1) + + (1|species),
 f_det = ~ uc1 + ec1 + (1|species),
 flocker_data = fd
)