contLikMLE2 {EFMrep} | R Documentation |
contLikMLE optimizes the likelihood function of the DNA mixture model
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)
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) |
ret A list from model fit
Oyvind Bleka