Get prior for occupancy model
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,
...
)A brms-type model formula for occupancy. If provided, must begin with "~".
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.
data, generally the output of make_flocker_data().
additional data (e.g. a covariance matrix for a phylogenetic effect)
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.
A brms-type model formula for colonization in colonization-extinction dynamic models. If provided, must begin with "~".
A brms-type model formula for extinction probabilities in colonization-extinction dynamic models. If provided, must begin with "~".
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.
Relevant only for autologistic models. A brms-type model formula for the autologistic offset parameter (theta). If provided, must begin with "~".
Logical. Must be TRUE if data are formatted for a data-augmented multi-species model, and FALSE otherwise.
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()
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.
sfd <- simulate_flocker_data()
fd <- make_flocker_data(
sfd$obs,
sfd$unit_covs,
sfd$event_covs
)
#> Formatting data for a single-season occupancy model. For details, see make_flocker_data_static. All warnings and error messages should be interpreted in the context of make_flocker_data_static
get_flocker_prior(
f_occ = ~ s(uc1) + + (1|species),
f_det = ~ uc1 + ec1 + (1|species),
flocker_data = fd
)
#> prior class coef group resp dpar nlpar lb ub
#> student_t(3, 0, 2.5) Intercept
#> (flat) b
#> (flat) b ec1
#> (flat) b uc1
#> student_t(3, 0, 2.5) sd 0
#> student_t(3, 0, 2.5) sd species 0
#> student_t(3, 0, 2.5) sd Intercept species 0
#> (flat) Intercept occ
#> (flat) b occ
#> (flat) b suc1_1 occ
#> student_t(3, 0, 2.5) sd occ 0
#> student_t(3, 0, 2.5) sd species occ 0
#> student_t(3, 0, 2.5) sd Intercept species occ 0
#> student_t(3, 0, 2.5) sds occ 0
#> student_t(3, 0, 2.5) sds s(uc1) occ 0
#> source
#> default
#> default
#> (vectorized)
#> (vectorized)
#> default
#> (vectorized)
#> (vectorized)
#> default
#> default
#> (vectorized)
#> default
#> (vectorized)
#> (vectorized)
#> default
#> (vectorized)