simulatetree: Simulate tree and sequences in two-population SIR-model
In Hackout3/saphy: Sequential Analysis of Phylogenies

Description Usage Arguments Value Author(s)

simulatetree does a deterministic simulation of a two-population SIR-model, takes samples and simulates a phylogenetic tree. For all this, it makes use of phydynR (https://github.com/emvolz-phylodynamics/phydynR). Then it simulates DNA-sequences for these samples, with simSeq (phangorn).

simulatetree(N = c(100, 10000), beta = array(c(1.5, 0, 0, 2, 1.5, 0, 0.1,
  2), dim = c(2, 2, 2)), gamma = 1, mu = 0.05, I0 = c(1, 1), t1 = c(50,
  100), res = 1000, sampletimes = c("incidence", "regular"),
  samplesize = 200, sampleperiod = c(0, tail(t1, 1)),
  sampledist = c("incidence", "popsize", "fixed"), samplebias = 1, ...)

`N`	the population sizes of the two populations
`beta`	an array of 2x2 transmission rate matrices. The third dimension is the number of matrices, which is the number of time intervals with different transmission rates. Transmission is modelled with frequency-dependent transmission terms (division by N).
`gamma`	the recovery rate
`mu`	the death rate. Births balance deaths.
`I0`	initial numbers of infecteds. The rest is assumed susceptible.
`t1`	a vector with times at which the transmission rates change to the next matrix in `beta`. The last time is the duration of the simulation
`res`	resolution of the epidemic simulation per transmission rate interval (ODE solver)
`sampletimes`	indicates if sampling occurs at random times proportional to incidence (default `"incidence"`) or at random uniform times (`"regular"`)
`samplesize`	the number of samples to be taken
`sampleperiod`	the time interval from which the sampling times should be taken
`sampledist`	indicates how samples should be divided over the two populations, apart from bias. The default `"incidence"` indicates proportionality to incidence; `"popsize"` indicates proportionality to population size; `"fixed"` indicates no proportionality, i.e. fifty-fifty
`samplebias`	indicates the extra weight (multiplication factor) given for sampling the first population relative to the second. If equal to 1, the weight is completely determined by `sampledist`.
`...`	arguments to be passed to simSeq (phangorn)