estimate_R_cl_rep {ern} | R Documentation |
Ensemble estimate of Rt
Description
Ensemble estimate of Rt
Usage
estimate_R_cl_rep(
cl.daily,
dist.repfrac,
dist.repdelay,
dist.incub,
dist.gi,
prm.R,
silent = FALSE,
RL.max.iter = 10
)
Arguments
cl.daily |
Dataframe of inferred daily incidence. |
dist.repfrac |
List. Parameters for the reporting fraction distribution in the same format as returned by |
dist.repdelay |
List. Parameters for the reporting delay distribution in the same format as returned by |
dist.incub |
List. Parameters for the incubation period distribution in the same format as returned by |
dist.gi |
List. Parameters for the generation interval distribution in the same format as returned by |
prm.R |
List. Settings for the ensemble when calculating Rt. Elements include:
|
silent |
Logical. Flag to suppress all output messages, warnings, and progress bars. |
RL.max.iter |
Integer. Maximum of iterations for the Richardson-Lucy deconvolution algorithm. |
Value
A summary of individual Rt realizations with 95% confidence intervals