withinCluster: test whether two cases are within the same transmission...

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

Description

test whether two cases are within the same transmission cluster

Usage

withinCluster(
  N,
  k_cutoff,
  t1,
  t2,
  lambda,
  beta,
  perc_cutoff,
  maxN = 25,
  N_resist = 0,
  lambda_resist = 0
)

Arguments

N	SNP distance
k_cutoff	number of transmissions below this threshold considered to be in same cluster
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
N_resist	number of resistance-conferring SNPs as a subset of N
lambda_resist	clock rate for resistance-conferring SNPs

Value

TRUE if within cluster, FALSE otherwise

Examples

isWithinCluster <- WithinCluster(N=5, k_cutoff=3, t1=2012.13, t2=2015.76, lambda=0.7, beta=1.3, perc_cutoff=0.2)

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