Tracer_Accumulation: Tracer Accumlation Function

In OJWatson/sims4: Epidemic generational simualator

Description

This slightly brute force function searches for all directories under a parent directory, assuming they were created with Generate_New_Sample_Data script, (see script for possible differences in directories and naming conventions for tracer exports) and collates the necessary summary statistics into one table.

Usage

Tracer_Accumulation(reps = 10, dirs = 15, vars = 5, var.R0 = TRUE,
  N.v = c(rep(10000, dirs)), mu.v = c(rep(0.001, 5), rep(1e-04, 5),
  rep(1e-05, 5)), Tg.v = c(rep(3, 15)), R0.v = c(rep(c(2, 3.5, 5, 10, 20),
  3)),
  root.dir = "C:/Users/Oliver/Google Drive/Academic Work/Imperial/O15-12/BEAST/Data Collection/Variable")

Arguments

reps	replicates total. Default = 10
dirs	number of subdirectories to be scanned
vars	variables total. Default = 5
var.R0	boolean for whether Generation_Sim or Broken was used in data creation. Default=TRUE
N.v	column vector of N. Default: N.v=c(rep(10000,reps)),
mu.v	column vector of mutation rates in directory. Default: mu.v=c(1e-04, rep(0.001,3), rep(1e-04,3), rep(1e-05,3)),
Tg.v	column vector of generation times in directory. Default: Tg.v=c(1,rep(3,9)),
R0.v	column vector of R0 in directory. Default: R0.v=c(2,rep(c(2,5,20),3)),
root.dir	- root directory, omitting a final /

Details

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

Value

Returns a data frame of collated statstics

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