getIncidentCases: Returns and/or plot numbers of sampled and unsampled cases...

In TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Description

Returns and/or plot numbers of sampled and unsampled cases over time

Usage

getIncidentCases(
  record,
  burnin = 0.5,
  numBins = 10,
  dateT = NA,
  show.plot = FALSE
)

Arguments

record	Output from inferTTree function
burnin	Proportion of the MCMC output to be discarded as burnin
numBins	Number of time bins to compute and display incident cases
dateT	Date when process stops (this can be Inf for fully resolved outbreaks)
show.plot	Show a plot of incident cases over time with stacked bars

Value

List with four entries. Time is a vector of the time points. allCases is the average number of cases at each time in the posterior. sampledCases: average number of sampled cases. unsampCases: average number of unsampled cases.

TransPhylo documentation built on April 20, 2021, 5:09 p.m.