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

calcINT

R Documentation

calcINT

Description

Marginalizing the likelihood through numerical integration.

Usage

calcINT(
  nC,
  samples,
  popFreq,
  lower = NULL,
  upper = NULL,
  refData = NULL,
  condOrder = NULL,
  knownRef = NULL,
  kit = NULL,
  DEG = TRUE,
  BWS = TRUE,
  FWS = TRUE,
  AT = 50,
  pC = 0.05,
  lambda = 0.01,
  fst = 0,
  knownRel = NULL,
  ibd = NULL,
  minF = NULL,
  normalize = TRUE,
  priorBWS = NULL,
  priorFWS = NULL,
  reltol = 0.001,
  scale = 0,
  maxEval = 0,
  verbose = FALSE,
  maxThreads = 0,
  adjQbp = FALSE
)

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.
`kit`	shortname of kit: Obtained from getKit()
`DEG`	Boolean of whether Degradation model should be used
`BWS`	Boolean of whether back-stutter model should be used
`FWS`	Boolean of whether for-stutter model should be used
`AT`	The analytical threshold given. Used when considering probability of allele drop-outs.
`pC`	A numeric for allele drop-in probability. Default is 0.
`lambda`	Parameter in modeled peak height shifted exponential model. Default is 0.
`fst`	is the coancestry coeffecient. Default is 0.
`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)
`minF`	The freq value included for new alleles (new alleles as potential stutters will have 0). Default NULL is using min.observed in popFreq.
`normalize`	Whether normalization should be applied or not. Default is FALSE.
`priorBWS`	Prior function for xi-parameter (stutter). Flat prior on [0,1] is default.
`priorFWS`	Prior function for xiFW-parameter (FW stutter). Flat prior on [0,1] is default.
`reltol`	Required relative tolerance error of evaluations in integration routine. Default is 0.001.
`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.
`verbose`	Whether printing limits to integrate over. Printing progress if maxEval>0. Default is TRUE.
`maxThreads`	Maximum number of threads to be executed by the parallelization
`adjQbp`	Indicate whether fragmenth length of Q-allele is based on averaged weighted with frequencies

Details

The procedure does numerical integration to approximate the marginal probability over the model parameters.

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.