Description Usage Arguments Value
View source: R/sequence.simulation.seqgen.par.R
Simulate sequence data of individuals in the transmissiion network using seq-gen tool
1 2 3 4 5 | sequence.simulation.seqgen.par(dir.seq = dir,
sub.dir.rename = sub.dir.rename, seq.gen.tool = "seq-gen",
simpact.trans.net = simpact.trans.net, seeds.num = 123, endpoint = 40,
limitTransmEvents = 3, hiv.seq.file = "hiv.seq.C.pol.j.fasta",
clust = TRUE)
|
dir.seq |
Direcotry where is the compiled seq-gen tool, sequences data may also be stored there |
sub.dir.rename |
sub directory where the simulation outputs will be stored |
seq.gen.tool |
Name of the file for compiled seq-gen |
simpact.trans.net |
Transmission network produced by |
seeds.num |
Seed number for reproducability |
endpoint |
Only transmission events that took place before this point in simulation time |
limitTransmEvents |
Minimum number of individuals in that transmission network (one transmission network per HIV seeding individual) |
hiv.seq.file |
File containing seed HIV sequences in FASTA format, it might be in same repository as seq-gen |
Files of sequences data, sampling dates, and transmission trees
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