nTransCutoff: create levels at which number of transmissions passes the...

In JamesStimson/transcluster: Transmission clustering using SNPs and sample dates

Description

create levels at which number of transmissions passes the threshold

Usage

nTransCutoff(
  N,
  t1,
  t2,
  lambda,
  beta,
  perc_cutoff,
  maxN = 25,
  maxK = 25,
  pSpatial = 1
)

Arguments

N	SNP distance
t1	date of first sample
t2	date of second sample
lambda	clock rate
beta	transmission rate
perc_cutoff	cut-off percentage
maxN	for optimisation, SNP distance greater than this considered not in same cluster

Value

number of transmissions reached

JamesStimson/transcluster documentation built on May 24, 2020, 10:39 p.m.