Prepare Stan Data from Real Tracking Dataset

Usage

prepare_stan_data(
  df,
  include_hab_cov = TRUE,
  include_ind_cov = TRUE,
  hab_cov_names = c("prey_avail", "hunter"),
  ind_cov_names = c("age", "sex_m"),
  include_cell_effect = TRUE,
  grid_bounds = NULL,
  grid_res = NULL,
  cause_col = "delta",
  n_causes = NULL,
  max_time_gap = Inf
)

Arguments

df: A data.frame containing GPS points with columns: x, y, animal_id, and any user-specified covariates
include_hab_cov: Logical; whether to include habitat covariates
include_ind_cov: Logical; whether to include individual-level covariates
hab_cov_names: Character vector of habitat covariate column names
ind_cov_names: Character vector of individual-level covariate column names
include_cell_effect: Logical; whether to include spatial cell effect
grid_bounds: Named list with xmin, xmax, ymin, ymax (only required if include_cell_effect = TRUE)
grid_res: Grid resolution in meters (required if include_cell_effect = TRUE), please make sure that the grid bounds are divisible by the grid resolution
cause_col: Character; name of the column in df that contains cause of death information
n_causes: Integer; number of unique causes of death (if applicable)
max_time_gap: Numeric; maximum time interval, in hours, allowed between consecutive GPS fixes. Intervals larger than this value are truncated to this value. The default is Inf, meaning that intervals are not truncated.

Value

A named list ready to be passed to a CmdStan model