sequoia: CalcBYprobs – R documentation

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CalcBYprobs

Birth year probabilities

Description

Estimate the probability that an individual with unknown birth year is born in year y, based on the (estimated) birth years of its parents and offspring and the age distribution of other parent-offspring pairs.

Usage

CalcBYprobs(Pedigree = NULL, LifeHistData = NULL, AgePrior = NULL)

Arguments

Pedigree

dataframe with columns id-dam-sire.

LifeHistData

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 ‘Pedigree’, nor do all individuals in the pedigree need to be included.

AgePrior

a matrix with probability ratios for individuals with age difference A to have relationship R, as generated by MakeAgePrior. If NULL, MakeAgePrior is called using its default values.

Details

This function assists in estimating birth years of individuals for which these are unknown, provided they have at least one parent or one offspring in the pedigree. It is not a substitute for field-based estimates of age, only a method to summarise the pedigree + birth year based information.

No distinction is made between genotyped and non-genotyped or dummy individuals.

Value

A matrix with for each individual (rows) in the pedigree that has a missing birth year in LifeHistData, or that is not included in LifeHistData, the probability that it is born in y (columns). Probabilities are rounded to 3 decimal points and may therefore not sum exactly to 1.

WARNING

Any errors in the pedigree or lifehistory data will cause errors in the birth year probabilities of their parents and offspring, and putatively also of more distant ancestors and descendants. If the ageprior is based on the same erroneous pedigree and lifehistory data, all birth year probabilities will be affected.

Examples

data(SeqOUT_griffin, package="sequoia")
BYprobs <- CalcBYprobs(Pedigree = SeqOUT_griffin$Pedigree,
                       LifeHistData = SeqOUT_griffin$LifeHist)

lattice::levelplot(t(BYprobs), aspect="fill", col.regions=hcl.colors)

sequoia

Pedigree Inference from SNPs

v2.3.3

GPL-2

Authors

Jisca Huisman [aut, cre]

Initial release

2021-04-30