Spatial_Generation_Sim: Spatial Generation epidemic genetic simulator
In OJWatson/sims4: Epidemic generational simualator

Description Usage Arguments Value Examples

This function starts with a root nucelotide sequence and evolves it via a spatial epidemic generational model. The result can then be used elsehere to generate newick trees and necessary enxus files for BEAUti/BEAST etc

Spatial_Generation_Sim(fasta.file = NULL, seq.length = 1000, spaces = 3,
  Nv = rep(100, spaces), dm = matrix(c(1, 1/100, 1/10000, 1/100, 1, 1/100,
  1/10000, 1/100, 1), nrow = 3, ncol = 3), mu = 1e-04, R0 = 3, Tg = 2,
  kappa = 2, model = "HKY85", I = 1, samples = 10)

`fasta.file`	path to a fasta sequence to be used as the root, otherwise random sequence used
`seq.length`	length of root sequence if not specified by fasta.file
`mu`	- mutation root in base changes per generation time
`R0`	- basic reproduction number
`Tg`	- mean generation time
`kappa`	- the rate of transitions and transversions
`model`	- substitution model - avaialble so far JC69, HKY85
`I`	- Initial infected space
`samples`	- 1/samples is equal to the random sample size of tips stored
`N`	- total popualation size, such that N-I = S

Returns a list of 9, with the first 7 lists giving the full infection network. As such res$ID[n] corresponds to res$Time/Parent/IsFather/Offspring/Branch.Length/Sequence/[n]. res$Seq and res$Seq.ID relate to eachother and the value within res$Sequence relates to res$Seq.ID and thus can be used to map a sequence to each individual