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

contLikSearch

R Documentation

contLikSearch

Description

contLikSearch search through the models which optimizes the likelihood function

Usage

contLikSearch(
  NOC = 2:3,
  modelDegrad = FALSE,
  modelBWstutt = FALSE,
  modelFWstutt = FALSE,
  samples = NULL,
  popFreq = NULL,
  refData = NULL,
  condOrder = NULL,
  knownRefPOI = NULL,
  prC = 0,
  nDone = 2,
  threshT = 50,
  fst = 0,
  lambda = 0,
  delta = 1,
  kit = NULL,
  verbose = TRUE,
  difftol = 0.01,
  knownRel = NULL,
  ibd = c(1, 0, 0),
  minF = NULL,
  normalize = TRUE,
  priorBWS = NULL,
  priorFWS = NULL,
  seed = NULL,
  maxThreads = 0,
  alpha = 0.01,
  steptol = 0.001,
  adjQbp = FALSE
)

Arguments

`NOC`	#The vector of number of contributors to search
`modelDegrad`	Whether degradation should be modeled (requires kit to be specified): can be vector (FALSE,TRUE)
`modelBWstutt`	Whether backward stutter should be modeled: can be vector (FALSE,TRUE)
`modelFWstutt`	Whether forward stutter should be modeled: can be vector (FALSE,TRUE)
`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.
`refData`	Reference objects with (2-size) allele-vector given in list element [[i]][[s]].
`condOrder`	condOrder under Hd. See calcMLE function for more details.
`knownRefPOI`	Specify index of known POI under Hp (can only be one number)
`prC`	A numeric for allele drop-in probability. Default is 0.
`nDone`	Number of optimizations required providing equivalent results (same logLik value obtained)
`threshT`	The detection threshold given. Used when considering probability of allele drop-outs.
`fst`	The co-ancestry coefficient. Default is 0.
`lambda`	Parameter in modeled peak height shifted exponential model. Default is 0.
`delta`	Scaling of variation of normal distribution when drawing random startpoints. Default is 1.
`kit`	Used to model degradation. Must be one of the shortnames of kit: check getKit()
`verbose`	Whether printing optimization progress. Default is TRUE.
`difftol`	Tolerance for being exact in log-likelihood value (relevant when nDone>1)
`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 BWS-parameter. Flat prior on [0,1] is default.
`priorFWS`	Prior function for FWS-parameter. Flat prior on [0,1] is default.
`seed`	The user can set seed if wanted
`maxThreads`	Maximum number of threads to be executed by the parallelization
`alpha`	The significance level used for the envelope test (validMLEmodel). Default is 0.01
`steptol`	Argument used in the nlm function for faster return from the optimization (tradeoff is lower accuracy).
`adjQbp`	Indicate whether fragmenth length of Q-allele is based on averaged weighted with frequencies