createModel: create model to be used for cluster analysis

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

Description

create model to be used for cluster analysis

Usage

createModel(
  ids = NULL,
  dates = NULL,
  snpMatrix = matrix(, 0, 0),
  lambda = 1,
  beta = 1,
  percCutOff = 0.2,
  thSNP = seq(1, 10),
  thTrans = seq(1, 10)
)

Arguments

ids	(optional) vector of unique sample IDs
dates	(optional) vector of dates (formatted as numbers)
snpMatrix	(optional) symmetric matrix of SNP distances supplied in the same order as ids
lambda	(optional) clock rate
beta	(optional) transmission rate
percCutOff	(optional) cut-off percentage
thSNP	(optional) SNP threshold values as a vector of integers
thTrans	(optional) transmission threshold values as a vector of integers

Value

model object for further analysis

Examples

myModel <- createModel()

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