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Set priors for the occARU model

set_priors.Rd

Constructs and validates a named list of prior hyperparameters for use with occARU(). Any unspecified priors use the defaults listed below.

Usage

set_priors(
  psi_bar = c(1, 1),
  q_bar = c(1, 3),
  mu_bar = c(1, 1),
  psi_W = c(3, 0, 1),
  mu_W = c(3, 0, 2.5),
  psi_theta = c(1, 1),
  mu_theta = c(1, 1),
  iota_ell = c(1, 1),
  kappa_ell = c(1, 1),
  kappa_ell_periodic = c(1, 1),
  K_phi = c(1, 1),
  nu_ell = c(1, 1),
  psi_iota_ell = c(1, 1),
  psi_nu_ell = c(1, 1),
  phi = c(0.4, 0.3),
  alpha_O_L = 1,
  psi_beta_O_L = 1,
  mu_beta_O_L = 1,
  gamma_O_L = 1,
  iota_O_L = 1,
  kappa_O_L = 1,
  nu_O_L = 1,
  psi_iota_O_L = 1,
  psi_nu_O_L = 1,
  epsilon_O_L = 1,
  verbose = TRUE
)

Arguments

psi_bar

Numeric vector of length 2. c(a, b) for a Beta(a, b) prior on mean occupancy probability. Default: c(1, 1).

q_bar

Numeric vector of length 2. c(shape, rate) for Gamma(shape, rate) priors on the mean annual colonisation and emigration rates for multiseason models. Default: c(1, 3).

mu_bar

Numeric vector of length 2. c(shape, rate) for a Gamma(shape, rate) prior on mean detection rate. Default: c(1, 1).

psi_W

Numeric vector of length 3. c(df, mu, sigma) for a Student-t+(df, mu, sigma) prior on total occupancy log odds variance. Default: c(3, 0, 1).

mu_W

Numeric vector of length 3. c(df, mu, sigma) for a Student-t+(df, mu, sigma) prior on total log detection variance. Default: c(3, 0, 2.5).

psi_theta

Numeric vector of length 2. c(shape, rate) for a Gamma(shape, rate) prior on the occupancy variance partition sparsity parameter. Default: c(1, 1).

mu_theta

Numeric vector of length 2. c(shape, rate) for a Gamma(shape, rate) prior on the detection variance partition sparsity parameter. Default: c(1, 1).

iota_ell

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on the detection spatial GP length scale. Default: c(1, 1).

kappa_ell

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on the temporal GP length scale. Default: c(1, 1).

kappa_ell_periodic

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on the periodic temporal GP length scale. Default: c(1, 1).

K_phi

Numeric vector of length 2. c(alpha[1], alpha[2]) for a Dirichlet(alpha) prior on the temporal GP variance partitions of the Matern and periodic kernels. Default: c(1, 1).

nu_ell

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on the detection season GP length scale. Default: c(1, 1).

psi_iota_ell

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on the occupancy spatial GP length scale. Default: c(1, 1).

psi_nu_ell

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on the occupancy season GP length scale. Default: c(1, 1).

phi

Numeric vector of length 2. c(alpha, beta) for an InvGamma(alpha, beta) prior on species-specific negative binomial overdispersion parameters. Default: c(0.4, 0.3).

alpha_O_L

Positive scalar. LKJ prior on the \([2, 2]\) occupancy log odds/log detection rate correlation matrix. Default: 1.

psi_beta_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific occupancy site coefficients. Only used when site predictors are supplied for occupancy in make_data(). Default: 1.

mu_beta_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific detection site coefficients. Only used when site predictors are supplied for detection in make_data(). Default: 1.

gamma_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific survey coefficients. Only used when survey predictors are supplied. Default: 1.

iota_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific site effects on detection. Default: 1.

kappa_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific survey effects. Default: 1.

nu_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific season effects on detection. Default: 1.

psi_iota_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific season effects on detection. Default: 1.

psi_nu_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific season effects on occupancy. Default: 1.

epsilon_O_L

Positive scalar. LKJ prior on the \([S, S]\) correlation matrix of species-specific OLRE residuals. Default: 1.

verbose

Logical. If TRUE (default), prints list of priors.

Value

An occARU_priors object (a named list) for use with occARU().

See also

occARU()