Compute Rt for a set of trajectories — carehomes_Rt

Compute "Rt" for a set of simulated trajectories (e.g., the result of dust::dust_iterate(), mcstate::pmcmc() or mcstate::pmcmc_predict(). The trajectories may or may not share parameters.

carehomes_Rt_trajectories(
  step,
  S,
  pars,
  initial_step_from_parameters = TRUE,
  shared_parameters = NULL
)

Arguments

step	A vector of steps
S	A 3d (19 x n trajectories x n steps) array of "S" compartment counts
pars	Either a single `carehomes_parameters()` object (shared parameters) or an unnamed list of `carehomes_parameters()` objects, the same length as `ncol(S)`.
initial_step_from_parameters	If `TRUE`, then `step[[1]]` is replaced by the value of `initial_step` from the parameters. This is usually what you want.
shared_parameters	Should `pars` be treated as a single shared list? Leave as `NULL` to detect automatically, set to `TRUE` or `FALSE` to force it to be interpreted one way or the other which may give more easily interpretable error messages.

As for carehomes_Rt(), except that every element is a matrix, not a vector.