contLikINT: contLikINT
In oyvble/euroformix: A Quantitative Model for Interpreting DNA Mixtures

contLikINT

R Documentation

contLikINT

Description

contLikINT marginalizes the likelihood through numerical integration.

Usage

contLikINT(
  nC,
  samples,
  popFreq,
  lower,
  upper,
  refData = NULL,
  condOrder = NULL,
  knownRef = NULL,
  xi = NULL,
  prC = 0,
  reltol = 0.01,
  threshT = 50,
  fst = 0,
  lambda = 0,
  pXi = function(x) 1,
  kit = NULL,
  scale = 0,
  maxEval = 0,
  knownRel = NULL,
  ibd = c(1, 0, 0),
  xiFW = 0,
  pXiFW = function(x) 1,
  maxThreads = 0,
  verbose = TRUE
)

Arguments

`nC`	Number of contributors in model.
`samples`	A List with samples which for each samples has locus-list elements with list elements adata and hdata. 'adata' is a qualitative (allele) data vector and 'hdata' is a quantitative (peak heights) data vector.
`popFreq`	A list of allele frequencies for a given population.
`lower`	Lower bounds of parameters. Must be in following order: mx1,..,mx_(nC-1),mu,sigma,beta,xi.
`upper`	Upper bounds of parameters. Must be in following order: mx1,..,mx_(nC-1),mu,sigma,beta,xi.
`refData`	Reference objects has locus-list element [[i]] with a list element 'r' which contains a 2 long vector with alleles for each references.
`condOrder`	Specify conditioning references from refData (must be consistent order). For instance condOrder=(0,2,1,0) means that we restrict the model such that Ref2 and Ref3 are respectively conditioned as 2. contributor and 1. contributor in the model.
`knownRef`	Specify known non-contributing references from refData (index). For instance knownRef=(1,2) means that reference 1 and 2 is known non-contributor in the hypothesis. This affectes coancestry correction.
`xi`	A numeric giving stutter-ratio if it is known. Default is NULL, meaning it is integrated out.
`prC`	A numeric for allele drop-in probability. Default is 0.
`reltol`	Required relative tolerance error of evaluations in integration routine. Default is 0.001.
`threshT`	The detection threshold given. Used when considering probability of allele drop-outs.
`fst`	is the coancestry coeffecient. Default is 0.
`lambda`	Parameter in modeled peak height shifted exponential model. Default is 0.
`pXi`	Prior function for xi-parameter (stutter). Flat prior on [0,1] is default.
`kit`	shortname of kit: Obtained from getKit()
`scale`	used to make integrale calculateable for small numbers. For scale!=0, integrale must be scaled afterwards with exp(-scale) to be correct.
`maxEval`	Maximum number of evaluations in the adaptIntegrate function. Default is 0 which gives an infinite limit.
`knownRel`	gives the index of the reference which the 1st unknown is related to.
`ibd`	the identical by decent coefficients of the relationship (specifies the type of relationship)
`xiFW`	A numeric giving FW stutter-ratio if it is known.Default is 0, meaning stutter is not used.
`pXiFW`	Prior function for xiFW-parameter (FW stutter). Flat prior on [0,1] is default.
`maxThreads`	Maximum number of threads to be executed by the parallelization
`verbose`	Whether printing limits to integrate over. Printing progress if maxEval>0. Default is TRUE.

Details

Replaced by new function calcINT

Value

ret A list(margL,deviation,nEvals,scale) where margL is Marginalized likelihood for hypothesis (model) given observed evidence, deviation is the confidence-interval of margL, nEvals is number of evaluations.