Helper function to create argument lists for common sampling scenarios, making it easier to work with the many parameters.
Usage
create_sampling_args(
pattern = "all",
seed,
custom = list(),
PATHS = NULL,
priors = NULL,
config = NULL
)Arguments
- pattern
Character string specifying the pattern. Options:
"all": The package default flags (every parameter except alpha_1, alpha_2, kappa and rho_deaths, which stay pinned)
"none": Don't sample any parameters
"disease_only": Sample only disease progression, immunity and reporting parameters
"transmission_only": Sample only the transmission rates (beta_j0_tot, p_beta)
"mobility_only": Sample only the mobility and diffusion parameters (mobility_omega, mobility_gamma, tau_i)
"spatial_only": Same flags as "mobility_only"; the spatial coupling of the model is its mobility network
"environmental_only": Sample only shedding and environmental decay (zeta_1, zeta_ratio, decay_*)
"initial_conditions_only": Sample only initial condition proportions
- seed
Random seed for sampling
- custom
Named list of flag overrides (e.g.
list(sample_kappa = TRUE)) applied after the pattern- PATHS
Optional PATHS object
- priors
Optional priors object
- config
Optional config object
Value
Named list of arguments suitable for do.call(sample_parameters, ...):
sample_args (a complete named list of logical flags), seed,
and PATHS, priors and config when supplied.
Details
Every pattern other than "all" sets each sample_* flag to FALSE except
the ones the pattern names. No pattern turns on a parameter the package pins
by default (alpha_1, alpha_2, kappa, rho_deaths);
re-enable one explicitly through custom. ic_moment_match keeps its default (FALSE)
unless set in custom. With every psi_star flag FALSE, the config's
psi_star values are still applied to psi_jt when they differ from the
identity transform (see sample_parameters).
Examples
if (FALSE) { # \dontrun{
# Sample only disease parameters
args <- create_sampling_args("disease_only", seed = 123)
config <- do.call(sample_parameters, args)
# Sample all except mobility
args <- create_sampling_args("all", seed = 123,
custom = list(sample_mobility_omega = FALSE,
sample_mobility_gamma = FALSE))
config <- do.call(sample_parameters, args)
} # }