contLikMLE2 {EFMrep}R Documentation

contLikMLE2

Description

contLikMLE optimizes the likelihood function of the DNA mixture model

Usage

contLikMLE2(nC, samples, popFreq, refData = NULL, condOrder = NULL,
  knownRef = NULL, kit = NULL, AT = 50, pC = 0.05, lambda = 0.01,
  fst = 0, mixProp = 1:length(samples), PHexp = 1:length(samples),
  PHvar = 1:length(samples), DEG = rep(0, length(samples)),
  stuttBW = rep(0, length(samples)), stuttFW = rep(0, length(samples)),
  minF = NULL, normalize = FALSE, maxIter = 100, steptol = 1e-06,
  nDone = 3, maxThreads = 128, delta = 1, seed = NULL,
  verbose = TRUE, knownRel = NULL, ibd = NULL)

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.

refData

Reference objects with (2-size) allele-vector given in list element [[i]][[s]].

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

A vector of kitname for each sample name, used to model degradation. Must be one of the shortnames of kit: check getKit()

AT

Analytical threshold. A vector per sample, or a list with marker elements per sample

pC

Dropin prob parameter. A vector per sample, or a list with marker elements per sample

lambda

DropinPH parameter. A vector per sample, or a list with marker elements per sample

fst

The co-ancestry coefficient. Default is 0. A vector per marker.

mixProp

Mixture proportion params: Indicate which shared parameter group each samples belongs to

PHexp

PeakHeight expectation params: Indicate which shared parameter group each samples belongs to

PHvar

PeakHeight variability params: Indicate which shared parameter group each samples belongs to

DEG

Degradation slope params: Indicate which shared parameter group each samples belongs to

stuttBW

Backward stutter params: Indicate which shared parameter group each samples belongs to

stuttFW

Forward stutter params: Indicate which shared parameter group each samples belongs to

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

A boolean of whether normalization should be applied or not. Default is FALSE.

maxIter

Maximum number of iterations for the optimization. Default is 100.

steptol

Argument used in the nlm function for faster return from the optimization (tradeoff is lower accuracy).

nDone

Number of optimizations required providing equivalent results (same logLik value obtained)

maxThreads

Maximum number of threads to be executed by the parallelization

delta

Scaling of variation of normal distribution when drawing random startpoints. Default is 1.

seed

The user can set seed if wanted

verbose

Boolean whether printing optimization progress. Default is TRUE.

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)

Value

ret A list from model fit

Author(s)

Oyvind Bleka


[Package EFMrep version 1.0.0 Index]