getIncidentCases {TransPhylo}

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

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.