calculate.cluster.size.moments.from.model: Calculate cluster size moments from model

In rcolgem: statistical inference and modeling of genealogies generated by epidemic and ecological processes

Description

Calculate cluster moments of the distribution of cluster sizes (clade sizes), which change as a function of the threhold TMRCA used for defining clades. Currently, only sampling at a single time point is supported.

Usage

  calculate.cluster.size.moments.from.model(sampleTime,
    sampleStates, maxTime = NA, minTime = NA,
    timeResolution = 50, discretizeRates = FALSE,
    fgyResolution = 100, integrationMethod = "adams")

Arguments

sampleTime	Time that sample is collected
sampleStates	(n X M) matrix of sample states for each taxon
maxTime
minTime
timeResolution	Determines time step for discrete approximations. Larger resolution gives smaller time step.
discretizeRates	if TRUE, a discrete approximation is used to calculate transition rates
fgyResolution	the number of time steps to use if discretizeRates=TRUE
integrationMethod	method passed to deSolve::ode

rcolgem documentation built on May 2, 2019, 5:28 p.m.