numeric matrix with genotype data: One row per individual, and one column per SNP, coded as 0, 1, 2 or -9 (missing). See also GenoConvert.

dataframe with 3 columns (optionally 5):

ID

max. 30 characters long

Sex

1 = female, 2 = male, 3 = unknown, 4 = hermaphrodite, other numbers or NA = unknown

BirthYear

birth or hatching year, integer, with missing values as NA or any negative value.

BY.min

minimum birth year, only used if BirthYear is missing

BY.max

maximum birth year, only used if BirthYear is missing

If the species has multiple generations per year, use an integer coding such that the candidate parents' ‘Birth year’ is at least one smaller than their putative offspring's. Column names are ignored, so ensure column order is ID - sex - birth year (- BY.min - BY.max). Individuals do not need to be in the same order as in ‘GenoM’, nor do all genotyped individuals need to be included.

list with output from a previous run, to be re-used in the current run. Used are elements ‘PedigreePar’, ‘LifeHist’, ‘AgePriors’, ‘Specs’, and ‘ErrM’, and these override the corresponding input parameters. Not all of these elements need to be present, and all other elements are ignored. If SeqList$Specs is provided, all input parameters with the same name as its items are ignored, except Module/MaxSibIter.

one of

pre

Only input check, return SeqList$Specs

dup

Also check for duplicate genotypes

par

Also perform parentage assignment (genotyped parents to genotyped offspring)

ped

(Also) perform full pedigree reconstruction, including sibship clustering and grandparent assignment. By far the most time consuming, and may take several hours for large datasets.

NOTE: Until 'MaxSibIter' is fully deprecated: if 'MaxSibIter' differs from the default (42), and 'Module' equals the default ('ped'), MaxSibIter overrides 'Module'.

[will be deprecated] number of iterations of sibship clustering, including assignment of grandparents to sibships and avuncular relationships between sibships. Clustering continues until convergence or until MaxSibIter is reached. Set to 0 for parentage assignment only.

estimated genotyping error rate, as a single number or 3x3 matrix. Details below. The error rate is presumed constant across SNPs, and missingness is presumed random with respect to actual genotype.

function that takes Err (single number) as input, and returns a 3x3 matrix of observed (columns) conditional on actual (rows) genotypes, or choose from inbuilt options 'version2.0', 'version1.3', or 'version1.1', referring to the sequoia version in which they were the default. Ignored if Err is a matrix. See ErrToM.

DEPRECATED AND IGNORED. Now calculated automatically using CalcMaxMismatch.

threshold log10-likelihood ratio (LLR) 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 LLR required for acceptance of proposed relationship, relative to next most likely relationship. Higher values result in more conservative assignments. Must be zero or positive.

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. Length 3 vector in case of hermaphrodites (or default prefix 'H').

Breeding system complexity. Either "full" (default), "simp" (simplified, no explicit consideration of inbred relationships), "mono" (monogamous).

Hermaphrodites, either "no", "A" (distinguish between dam and sire role, default if at least 1 individual with sex=4), or "B" (no distinction between dam and sire role). Both of the latter deal with selfing.

either "yes" (default), "no", or "extra" (additional rounds with extra reliance on ageprior, may boost assignments but increased risk of erroneous assignments); used during full reconstruction only.

list with arguments to be passed on to MakeAgePrior.

DEPRECATED AND IGNORED, advised to run GetMaybeRel separately. TRUE/FALSE to identify pairs of non-assigned likely relatives after pedigree reconstruction. Can be time-consuming in large datasets.

TRUE/FALSE; calculate log-likelihood ratios for all assigned parents (genotyped + dummy; parent vs. otherwise related). Time-consuming in large datasets. Can be done separately with CalcOHLLR.

suppress messages: TRUE/FALSE/"verbose".

display plots from SnpStats, MakeAgePrior, and SummarySeq. Defaults (NULL) to TRUE when quiet=FALSE or "verbose", and FALSE when quiet=TRUE. If you get error 'figure margins too large', enlarge the plotting area (drag with mouse). Error 'invalid graphics state' can be dealt with by clearing the plotting area with dev.off().

Matrix with age-difference based probability ratios for each relationship, used for full pedigree reconstruction; see MakeAgePrior for details. When running only parentage assignment (Module="par") the returned AgePriors has been updated to incorporate the information of the assigned parents, and is ready for use during full pedigree reconstruction.

Dataframe with pedigree for dummy individuals, as well as their sex, estimated birth year (point estimate, upper and lower bound of 95% confidence interval; see also CalcBYprobs), number of offspring, and offspring IDs. From version 2.1 onwards, this includes dummy offspring.

Dataframe, duplicated genotypes (with different IDs, duplicate IDs are not allowed). The specified number of maximum mismatches is used here too. Note that this dataframe may include pairs of closely related individuals, and monozygotic twins.

Dataframe, row numbers of duplicated IDs in life history dataframe. For convenience only, but may signal a problem. The first entry is used.

Error matrix; probability of observed genotype (columns) conditional on actual genotype (rows)

Individuals in GenoM which were excluded because of a too low genotyping success rate (<50%).

Column numbers of SNPs in GenoM which were excluded because of a too low genotyping success rate (<10%).

Provided dataframe with sex and birth year data.

LifeHist with additional columns 'Sexx' (inferred Sex when assigned as part of parent-pair), 'BY.est' (mode of birth year probability distribution), 'BY.lo' (lower limit of 95% highest density region), 'BY.hi' (higher limit), inferred after parentage assignment. 'BY.est' is NA when the probability distribution is flat between 'BY.lo' and 'BY.hi'.

as LifeHistPar, but estimated after full pedigree reconstruction

Dataframe with pairs of individuals who are more likely parent-offspring than unrelated, but which could not be phased due to unknown age difference or sex, or for whom LLR did not pass Tassign.

Dataframe with pairs of individuals who are more likely to be first or second degree relatives than unrelated, but which could not be assigned.

Dataframe with non-assigned parent-parent-offspring trios (both parents are of unknown sex), with similar columns as the pedigree

Vector, IDs in genotype data for which no life history data is provided.

Dataframe with assigned genotyped and dummy parents from Sibship step; entries for dummy individuals are added at the bottom.

Dataframe with assigned parents from Parentage step.

Named vector with parameter values.

Numeric vector, Total likelihood of the genotype data at initiation and after each iteration during Parentage.

Numeric vector, Total likelihood of the genotype data at initiation and after each iteration during Sibship clustering.

As AgePriors, but including columns for grandparents and avuncular pairs. NOT updated after parentage assignment, but returned as used during the run.

Hermaphrodites only: female-male dummy ID pairs that refer to the same non-genotyped individual

Individual ID

Assigned mother, or NA

Assigned father, or NA

Log10-Likelihood Ratio (LLR) of this female being the mother, versus the next most likely relationship between the focal individual and this female. See Details below for relationships considered, and see CalcPairLL for underlying likelihood values and further details)

idem, for male parent

LLR for the parental pair, versus the next most likely configuration between the three individuals (with one or neither parent assigned)

Number of loci at which the offspring and mother are opposite homozygotes

idem, for father

Number of Mendelian errors between the offspring and the parent pair, includes OH as well as e.g. parents being opposing homozygotes, but the offspring not being a heterozygote. The offspring being OH with both parents is counted as 2 errors.