BEAST_R0_Full: BEAST_R0_Full

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

Description

Main simulation function to investigate the effects of sampling strategy against TMRCA/Clock Rate Bias. As opposed to BEAST_R0_Check, this function considers all sampling schemes.

Usage

BEAST_R0_Full(N = 1e+05, R0 = 2, Tg = 2, t.cont = TRUE,
  real.time = FALSE, scale = 1, size.reps = c(0, 10, 1, 0.1),
  mu = 1.57e-05, root.path = NULL, seq.length = 1600, model = "HKY85",
  evolution.model = "within.host", kappa = 2, outgroup = FALSE,
  missed.generations = 0, n.seq.samples = 50, sample.reps = 10,
  tree.reps = 20, sigma.reps = c(1, 5, 9, 13, 18), oldestboolean = FALSE,
  template.xml = "C:/Users/Oliver/GoogleDrive/AcademicWork/Imperial/git/evoflution/inst/extdata/template.xml",
  dir = "C:/Users/Oliver/GoogleDrive/AcademicWork/Imperial/git/evoflution/Results/Within_Host_No_Outgroup",
  network.path = "\\\\fi--san02.dide.ic.ac.uk\\homes\\olw13\\Data\\")

Arguments

N	Target infected population size. Default = 1e5
R0	basic reproduction number. Default = 2
Tg	mean generation time. Default = 2.6 days
t.cont	Boolean dictating whether gamma process is used for generation time distribution. Default = TRUE
real.time	Boolean dictating. whether an extra generation is simulated producing extra for real.time consideration.Default = FALSE
scale	rgamma scale parameter. Default = 1
size.reps	Vector of different size parameters in negative binomial offspring distribution. Default=c(0,10,1,0.1)
mu	Clock Rate. Default=1e-4
root.path	File path of saveRDS(root). Default = NULL
seq.length	Sequence length. Will be overwritten accordingly if root.path given. Default = 1701
model	Nucleic subsitution model. Can be one of "JC69", "K80", "HKY85" (Default)
evolution.model	String variable detailing evolutionary model. Can be any of "generational", "within.host" and "parallel"
kappa	Tv/Ts ration. Default = 2
missed.generations	Number of intiial generations not considered for sampling. Default = 0
n.seq.samples	number of sequences to be sampled. Default = 50
sample.reps	number of tree subsamples under each scheme. Default = 10
tree.reps	number of unique tree simulations conducted under each scheme. Default = 20
sigma.reps	variables total. Default = c(1,5,9,13,18)
oldestboolean	boolean if oldest sequence not root is included. Default=TRUE
template.xml	path for template xml. Default is a strict molecular clock, exponential coalescent, HKY85+G4 xml found within the data folder called test.xml
dir	Local Directory where simulations tree and nexus files are stored. Defaults specific to author.
network.path	Network Directory which a cluster can see to access the BEAST xml files. Defaults specific to author.
size.reps	- Vector of offspring distribution parameters. Default=c(0,10,1,0.1)
outgoup	Boolean concerning whether outgroup is simulated. Default = FALSE

Details

BEAST_R0_Full proceeds by simulating a tree in a local directory, sampling from it and placing the nexus samples within the local directory, before then creating the BEAST2.3xml file in a parallel network directory, and then running the BEAST analysis using the batch collation file.

Highly prescriptive function declaration, which considers all the simulation parameters needed, the range of sigma parameters, the BEAST template required, directories etc.

Value

Returns a data frame of collated statstics

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