New_sampling: Forwards genetic sequence simulator

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

Description

New_sampling uses the output of Infection_Sim and Sequencing to sample a selection of sequences and write the annotated output top file as a fasta

Usage

New_sampling(sim.out, seq.out, file, n.seq.samples = 50, bs.label = "rep",
  sigma = 1, n.bs = 50, random = TRUE, oldestboolean = TRUE,
  outgroup = TRUE, discretised = FALSE, proportional = FALSE,
  t.cont = TRUE, missed.generations = 0)

Arguments

sim.out	Output of Infection_Sim
seq.out	Output of Sequencing
file	Directory path where the nexus file of samples are to be saved to.
n.seq.samples	Number of sequences to be sampled in total
bs.label	String used to be added on to the created nex files. Default = "bs"
sigma	The interval parameter, where the interval of sequences is equal to 1/sigma. Default = 1, i.e. all sequences
n.bs	Number of bootstrap samples to create. Default = 50
oldestboolean	Boolean if the oldest sample is included (TRUE). Default=TRUE
outgroup	Boolean if the outgroup is included (TRUE). Default=FALSE
discretised	Boolean if discretised sampling occurs. Default = FALSE
proportional	Boolean if proportional sampling occurs. Default = FALSE
t.cont	Boolean if the simulation occurs in discrete (FALSE) or continuous time (TRUE), in turn directing whether decimilisation is needed in uniform sampling strategies.
missed.generations	Number of intiial generations not considered for sampling. Default = 0

Value

save a nexus file of dated sequences

Note

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