Append summaries of outbreaker results to a linelist

For each case in linelist, appends summary statistics of selected parameters from an outbreaker_chains object (e.g. infection times, number of generations).

Usage

augment_linelist(
  out,
  linelist,
  params = c("t_inf", "kappa"),
  summary_fns = list(mean = function(x) mean(x, na.rm = TRUE), q25 = function(x)
    quantile(x, 0.25, na.rm = TRUE), q75 = function(x) quantile(x, 0.75, na.rm = TRUE))
)

Arguments

out

An outbreaker_chains object containing posterior samples.

linelist

A data.frame with an id column matching the IDs in out.

params

Character vector of parameter prefixes to summarise (e.g. "t_inf", "kappa").

summary_fns

A named list of summary functions. Each function takes a numeric vector and returns a single value. Example: list( mean = function(x) mean(x, na.rm = TRUE), q25 = function(x) quantile(x, 0.25, na.rm = TRUE), q75 = function(x) quantile(x, 0.75, na.rm = TRUE) )

Value

The input linelist, with new columns named <param>_<fn> (e.g. t_inf_mean, kappa_q25).

Examples

augmented_linelist <- augment_linelist(
  out, linelist,
  params = c("t_inf", "kappa"),
  summary_fns = list(
    median = function(x) median(x, na.rm = TRUE),
    q25 = function(x) quantile(x, 0.25, na.rm = TRUE),
    q75 = function(x) quantile(x, 0.75, na.rm = TRUE)
  )
)