Compute Rt for a set of trajectories — lancelot_Rt

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

lancelot_Rt_trajectories(
  time,
  S,
  pars,
  prob_strain = NULL,
  initial_time_from_parameters = TRUE,
  shared_parameters = NULL,
  type = NULL,
  interpolate_every = NULL,
  interpolate_critical_dates = NULL,
  interpolate_min = NULL,
  eigen_method = "power_iteration",
  R = NULL,
  weight_Rt = FALSE,
  keep_strains_Rt = FALSE
)

Arguments

time: A vector of time steps
S: A 3d ((n groups x n vaccine classes) x n trajectories x n time steps) array of "S" compartment counts
pars: Either a single lancelot_parameters() object (shared parameters) or an unnamed list of lancelot_parameters() objects, the same length as ncol(S).
prob_strain: A 3d ((n groups x n strains) x n trajectories x n time steps) array of "prob_strain" model outputs. Default is NULL, but it must be specified if there is more than one strain.
initial_time_from_parameters: If TRUE, then time[[1]] is replaced by the value of initial_time from the parameters. This is usually what you want. (From sircovid 0.12.13 this parameter means "initial time is zero" and will probably be updated in a future version).
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.
type: A character vector of possible Rt types to compute. Can be any or all of eff_Rt_all, eff_Rt_general, Rt_all and Rt_general
interpolate_every: Spacing (in days) to use between interpolated points
interpolate_critical_dates: Optional vector of critical sircovid dates to use when interpolating. Interpolation will be done in blocks between the first time step of these dates, with each block starting on the first time step of the date given. So if you give a interpolate_critical_dates of c(20, 50) then blocks start on first time step of days 20 and 50, i.e.: [1, 20), [20, 50), [50, end].
interpolate_min: The minimum number of steps to include within a block. If there are fewer points than this then all points are used (i.e., no interpolation is done) or interpolate_every is reduced until at least this many points were used. This can be used to specify a lower bound on the error of small regions. If Rt is small it won't matter that much. You do need to specify something though or interpolation will not happen, and do not use less than 3 as we use spline interpolation and that will not work with fewer than 3 points.
eigen_method: The eigenvalue method to use (passed to eigen1::eigen1 as method)
R: A 3d ((n groups x n strains x n vaccine classes) x n trajectories x n time steps) array of "R" compartment counts, required for multi-strain models.
weight_Rt: If TRUE then computes the weighted average of the Rt for all strains, otherwise all calculations are returned with an additional dimension to index each strain.
keep_strains_Rt: Additional argument for when weight_Rt is TRUE (has no impact otherwise). If TRUE, then the Rt for each strain is returned along with the weighted average, otherwise just the weighted average is returned. When TRUE, the dimension indexing these lists strains first, and then the weighted average.

Value

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