TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

View source: R/interpret.R View source: R/extras/getIncidentCases.R

getIncidentCases

R Documentation

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.

xavierdidelot/TransPhylo documentation built on Sept. 28, 2023, 7:20 p.m.