Tip_Samples: Tip Sampling Procedure
In OJWatson/sims4: Epidemic generational simualator

Description Usage Arguments Value Note

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.

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Tip_Samples(case.tree, file, n.tips = length(case.tree$Seq.ID),
  all.clades = TRUE, prop.clades = 0.5, extant = TRUE, bias = FALSE,
  prop.times = 1)

`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 save to
`n.tips`	the numer of tips to chosen in total
`all.clades`	boolean determining if all extant clades have to be sampled. Default = TRUE
`prop.clades`	if all.clades==FALSE, prop.clades specifies the proportion of clades to be sampled
`extant`	boolean determining if only extant tips are chosen. Default = TRUE. An extant tip is simply a case that was yet to be chosen to be a parent or not at the end of the simulation
`prop.times`	if extant = FALSE determines over what case network time window samples are to be chosen by. As such, prop.times can only take a value between 0 and 1, whereby 1 would mean all cases could be sampled at random, and 0.5 would mean only the most recent half of the cases could be sampled. An error will throw if prop.times*length(case.tree$ID)<n.tips, i.e. more tips than possible given sampling time window.

a nexus file of dated tips with sequences

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.