Check parameter values and save as named vector.
SeqPrep(GenoM = NULL, LifeHistData = NULL, nAgeClasses = 1,
MaxSibIter = 5, Err = 1e-04, MaxMismatch = 3, Tfilter = -2,
Tassign = 0.5, MaxSibshipSize = 100, DummyPrefix = c("F", "M"),
Complexity = "full", UseAge = "yes", FindMaybeRel = TRUE,
CalcLLR = TRUE)matrix with genotype data, size nInd x nSnp
Dataframe with 3 columns:
ID: max. 30 characters long,
Sex: 1 = females, 2 = males, other numbers = unkown,
Birth Year: (or hatching year) Zero and negative numbers are interpreted as missing values.
Number of age classes (= no. rows in AgePriors)
Maximum number of iterations of sibship clustering (up to 42).
Estimated genotyping error rate.
Maximum number of loci at which candidate parent and offspring are allowed to be opposite homozygotes, or be excluded.
Threshold log-likelihood ratio between a proposed relationship versus unrelated, to select candidate relatives. Typically a negative value, related to the fact that unconditional likelihoods are calculated during the filtering steps. More negative values may decrease non-assignment, but will increase computational time.
Minimum log-likelihood ratio required for acceptance of proposed relationship, relative to next most likely relationship. Higher values result in more conservative assignments.
Maximum number of offspring for a single individual (a generous safety margin is advised).
character vector of length 2 with prefixes for dummy dams (mothers) and sires (fathers); maximum 20 characters each.
Either "full" (default), "simp" (no explicit consideration of inbred relationships), "mono" (monogamous breeding system), or "herm" (hermaphrodites)
Identify pairs of non-assigned likely relatives after pedigree reconstruction. Can be time-consuming in large datasets.
Calculate log-likelihood ratios for all assignments. Can be time-consuming in large datasets.
A 1-row dataframe with parameter values
Please do not increasing the number of SNPs or individuals beyond the numbers present in the datasets, as this may cause R to crash.