BEAST_R0_Network_Pull_Tracer: BEAST_R0_Network_Pull_Tracer

In OJWatson/evoflution: Forward in time epidemic and genetic simulator with a focus on flu

Description

Summary Statistics are clock rate, growthRate, ePop and TMRCA.

Usage

BEAST_R0_Network_Pull_Tracer(sampling.reps = 20, rep.name = "bs",
  outgroup = FALSE, tree.reps = 10, vars = 5, var.R0 = 0, sigma = 1,
  N.v = c(rep(1e+05, tree.reps)), mu.v = c(rep(1.57e-05, tree.reps)),
  Tg.v = c(rep(2.6, tree.reps)), R0.v = c(rep(2, tree.reps)),
  network.root.dir, local.root.dir)

Arguments

sampling.reps	Sampling replicates total. Default = 20
rep.name	The character name used for each sampling rep, i.e. Unifrom, Random, Oldest_Bar_One
outgroup	Boolean describing if an outgroup was present
tree.reps	number of subdirectories to be scanned
vars	Tracer variables t collect in total. Default = 5
var.R0	Size parameter for offspring distribtuion. Default = 0
sigma	value Sigma value used
N.v	column vector of N. Default: N.v=c(rep(100000,tree.reps)),
mu.v	column vector of mutation rates in directory. Default: mu.v=c(rep(1.57e-05,tree.reps)),
Tg.v	column vector of generation times in directory. Default: Tg.v=c(rep(2.6,tree.reps)),
R0.v	column vector of R0 in directory. Default: R0.v=c(rep(2,tree.reps)),
network.root.dir	network root directory
local.root.dir	local root directory

Value

Returns a data frame of collated statstics

OJWatson/evoflution documentation built on May 7, 2019, 8:32 p.m.