Make data for DRM stan models

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

Usage

make_data(
  y,
  time,
  site,
  init_data = numeric(0),
  f_mort,
  m = -log(0.7),
  x_t,
  x_m,
  x_r,
  n_ages = 2,
  age_selectivity,
  ages_movement,
  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

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

site

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

init_data

an optional vector (of lengh n_ages - 1) to initialize the population dynamics.

f_mort

an optional matrix informing the instantaneous fishing mortality rates at each age (columns) and timepoint (rows).

m

a numeric value corresponding to the instantaneous natural mortality rate. The default value for this is -log(.7), as it implies a survival rate of 0.70 between age classes.

x_t

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

x_m

a design matrix of variables associated to survival.

x_r

a design matrix of variables associated to recruitment.

n_ages

an integer indicating the number of ages for the underlying population dynamic model.

age_selectivity

an numeric vector with n_ages elements, where each element indicates the selectivity of a respective age. All the elements of this vector must lie between 0 and 1.

ages_movement

An integer or a numeric vector specifying the ages at which individuals of the focal species are assumed to move. If ages_movement is an integer, individuals younger than this age are considered static (non-moving). If ages_movement is a numeric vector of length n_ages, it indicates movement capability for each age group. A value of 0 indicates the corresponding age group is static, while 1 indicates movement is allowed. For example, c(0, 0, 1, 1, 0) specifies that age groups 1, 2, and 5 are static, while 3 and 4 are mobile.

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:

• rho_mu: 1 to use explicitly relates rho to mu and 0 otherwise.

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

• movement: 1 to allow for (adjacent) moviment; 0 for static.

• est_surv: 1 to estimate mortality and 0 otherwise.

• est_init: 1 to estimate initial values for lambda and 0 otherwise.

• minit: 1 to use mortality to estimate initial age classes and 0 otherwise.

• ar_re: a character. It assumes one of the following values: "none" - no AR, "rec" AR(1) for recruitment, "surv" - AR(1) for survival (only works when est_surv is on), "dens" - AR(1) for density.

• iid_re: a character. It assumes one of the following values: "none" - no iid re, "rec" iid re for recruitment, "surv" - iir re for survival (only works when est_surv is on), "dens" - iid_re for density.

• sp_re: a character. It assumes one of the following values: "none" - no ICAR re, "rec" ICAR re for recruitment, "surv" - ICAR re for survival (only works when est_surv is on), "dens" - ICAR_re for density.

.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 mean.

• "lognormal_legacy" (default): 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.

Value

a list to be used as the input for a stan model

Author

lcgodoy