Seqgen_Validation: seqgen validation of sims4 sequence evolution

In OJWatson/sims4: Epidemic generational simualator

Description

This function creates the potential perfect bifurcating tree with equal branch lengths of Tg and always R0 offspring, i.e if R0 = 2, by using the Broken_Generation_Sim function that assumes these facts. This tree is then stored. Comapritive model validation occurs by simulating this same tree with the same Broken_Generation_Sim function and recording the number of unique sequences at the tips, while also calculating the same value but by using seqgen, before returning tse

Usage

Seqgen_Validation(reps = 10, seq.length = 1000, mu = 1e-04, N = 127,
  Tg = 1, kappa = 2, R0 = 2, t.exp = TRUE, model = "HKY85")

Arguments

case_tree

the case tree generated from a simulator function within sims4

Value

Returns a distribution of estimated TMRCA

OJWatson/sims4 documentation built on May 7, 2019, 8:33 p.m.