Make data for SDM stan models

This function creates the list used as the input for the stan model.

Usage

make_data_sdm(
  y,
  time,
  site,
  z,
  x,
  adj_mat = matrix(0, ncol = 1, nrow = 1),
  .toggles,
  .priors,
  family = "gamma",
  reorder = TRUE,
  phi_hat = FALSE
)

Arguments

y

a numeric vector of species' densities.

time

a vector indicating the time point associated to each element of y.

site

a vector indicating the sites associated to each element of y.

z

a design matrix of variables associated to the probability of absence at each site/time.

x

a design matrix of variables associated to the non-zero densities.

adj_mat

an adjacency matrix of dimensions sites \(\times\) sites. Its elements are 1 if two sites are neighbors and zero otherwise.

.toggles

a list of toggles for model components. The components are:

• cloglog: 1 to use the complementary log-log and 0 for the logit link function for the absence probabilities.

• ar_re: 1 to incorporate an AR(1) process to density and 0 otherwise.

• iid_re: 1 to incorporate a site specific IID random effect to density and 0 otherwise.

• sp_re: 1 to incorporate a site specific ICAR random effect to density and 0 otherwise.

.priors

a list of priors hyperparameters.

family

a character specifying the family of the probability distribution assumed for density. The options are:

• "gamma" (default): gamma parametrized in terms of its mean;

• "lognormal": log-normal parametrized in terms of its mean;

• "loglogistic": log-logistic parametrized in terms of its median (usual parametrization);

• "lognormal_legacy": log-normal with its usual parametrization;

reorder

a boolean telling whether the data needs to be reordered. The default is TRUE and means the data points will be ordered by site and time, respectively.

phi_hat

a boolean indicating whether the prior on phi should be determined through the data (using get_phi_hat()).

Value

A list containing the data and settings to be used as input for the Stan model.

Author

lcgodoy