paternity: Estimates fractional paternity probability
In dyerlab/gstudio: Tools Related to the Spatial Analysis of Genetic Marker Data

paternity

R Documentation

Estimates fractional paternity probability

Description

This function estimates fractional paternity for offspring given a set of potential fathers.

Usage

paternity(
  offspring,
  mother,
  fathers,
  ID = "ID",
  OffID = "OffID",
  strict = FALSE
)

Arguments

`offspring`	A particular offspring. Often as a row from a `data.frame` with columns as loci and other meta data.
`mother`	The assumed mother of the offspring as a row from a `data.frame` with columns as loci and other meta data.
`fathers`	A `data.frame` of potential fathers.
`ID`	The name of the column where the dad's adult ID column is found in the `data.frame` of potential fathers.
`OffID`	The name of the column where the offspring ID is located. All offspring from a maternal individual should have have the same maternal `ID` to indicate which mother they are from but must also have a unique offspring ID.
`strict`	A flag (default=FALSE) to use strict paternity (e.g., where only one dad can be the father) versus fractional paternity (e.g., where potentially more than one father is assignable but whose likelihood is based upon their transition probabilities).

Value

A data.frame with indications of paternity by row. Columns will include ID, OffID, DadID, and potentially Fij.

Author(s)

Rodney J. Dyer rjdyer@vcu.edu

Examples

freqs <- c(1/3,1/3,1/3)
loci <- rep( paste("Loc",1:6,sep="-"), each=3)
alleles <- LETTERS[1:3]
f <- data.frame(Locus=loci, Allele=alleles, Frequency=freqs)
f
adults <- make_population(f,N=20)
adults
offs <- mate( adults[1,], adults[2,], N=10)
offs$OffID <- offs$ID
offs$MomID <- adults$ID[1]
paternity( offs, adults[1,], adults )

dyerlab/gstudio documentation built on Feb. 2, 2024, 8:24 p.m.