enw_replace_priors: Replace default priors with user specified priors

In seabbs/epinowcast: Flexible Hierarchical Nowcasting

Replace default priors with user specified priors

Description

This function is used internally by epinowcast to replace default model priors with users specified ones (restricted to normal priors with specified mean and standard deviations). A common use would be extracting the posterior from a previous epinowcast() run (using summary(nowcast, type = fit)) and using this a prior.

Usage

enw_replace_priors(priors, custom_priors)

Arguments

priors	A data.frame with the following variables: variable, mean, sd describing normal priors. Priors in the appropriate format are returned by enw_reference() as well as by other similar model specification functions.
custom_priors	A data.frame with the following variables: variable, mean, sd describing normal priors. Priors in the appropriate format are returned by enw_reference() as well as by other similar model specification functions. Priors in this data.frame replace the default priors. Note that currently vectorised prior names (i.e those of the form variable[n] will be treated as variable).

Value

A data.table of prior definitions (variable, mean and sd).

See Also

Functions used to help convert models into the format required for stan enw_formula_as_data_list(), enw_get_cache(), enw_model(), enw_pathfinder(), enw_priors_as_data_list(), enw_sample(), enw_set_cache(), enw_stan_to_r(), enw_unset_cache(), remove_profiling(), write_stan_files_no_profile()

Examples

# Update priors from a data.frame
priors <- data.frame(variable = c("x", "y"), mean = c(1, 2), sd = c(1, 2))
custom_priors <- data.frame(variable = "x[1]", mean = 10, sd = 2)
enw_replace_priors(priors, custom_priors)

# Update priors from a previous model fit
default_priors <- enw_reference(
 distribution = "lognormal",
 data = enw_example("preprocessed"),
)$priors
print(default_priors)

fit_priors <- summary(
 enw_example("nowcast"), type = "fit",
 variables = c("refp_mean_int", "refp_sd_int", "sqrt_phi")
)
fit_priors

enw_replace_priors(default_priors, fit_priors)

seabbs/epinowcast documentation built on Oct. 8, 2024, 8:35 p.m.