make_starting_trees: Make starting trees and ML tree plot

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

This will generate multiple starting trees by ML & treedater. Each tree is produced by a different random resolution of polytomies in the ML tree Sequence names must have sample times included (see prep_tip_labels)

Usage

make_starting_trees(
  fastafn,
  treeoutfn = "startTrees.nwk",
  plotout = NULL,
  regionDemes = c("Il"),
  ntres = 1,
  ncpu = 4
)

Arguments

fastafn	File name of sequence data (needed for ML tree estimation)
treeoutfn	File name of trees to be written
plotout	File name of ML tree plot. set to Null to not plot
regionDemes	demes to colour in the output tree plot
ntres	integer how many start trees to produce? a distinct xml is made for each
ncpu	Number of CPUs to use

Value

Some treedater trees. New start trees are written to disk. ML tree plot written to disk

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.