Optimised_Tip_Samples: Sampling Optimisation Sample Creation

In OJWatson/sims4: Epidemic generational simualator

Description

This function uses the case network produced by any of the sims4 smulators and produces a set of dated tip sequences. The distribution and number of tips are declared as variables, with the default case choosing 1 extant tip from each clade. The effect of this being to make the easiest generation of the correct TMRCA by BEAST, with the least amount of computatonal demand.

Usage

Optimised_Tip_Samples(case.tree, file, n.tips = length(case.tree$Seq.ID),
  sigma = 1, bs = FALSE, n.bs = n.tips, sample = TRUE,
  oldestboolean = TRUE)

Arguments

case.tree	the case tree generated from a simulator function within sims4
file	the path name where the nexus file of samples is to be saved to. If bs is TURE this should be the directory
n.tips	the numer of tips to be chosen in total
sigma	the interval parameter, where the interval of tips is equal to 1/sigma. Default = 1, i.e. all tips
bs	whether bootstrapping of the sampel set occurs. Deafult = FALSE
n.bs	number of bootstrap samples to create. Default = n.tips

Value

save a nexus file of dated tips with sequences

Note

If the combination of prop.times and extant==FALSE creates a time window that does not include all clades, and all.clades == TRUE, only all the possible clades within the time window will be sampled.

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