createPedTree: Create a pedigree tree (PedTree).

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Description

The PedTree is a list containing sire and dam information for an individual.

Usage

createPedTree(ped)

Arguments

ped	dataframe of pedigree and demographic information potentially containing columns indicating the birth and death dates of an individual. The table may also contain dates of sale (departure). Optional columns are birth, death, departure.

Details

Part of Pedigree Sampling From PedigreeSampling.R 2016-01-28

Contains functions to build pedigrees from sub-samples of genotyped individuals.

The goal of sampling is to reduce the number of inbreeding loops in the resulting pedigree, and thus, reduce the amount of time required to perform calculations with SIMWALK2 or similar programs.

This function uses only id, sire, and dam columns.

Value

A list of named lists forming a pedigree tree (PedTree or ptree). Each sublist represents an ID in the pedigree and contains the sire ID and the dam ID as named elements.

Examples

library(nprcgenekeepr)
exampleTree <- createPedTree(nprcgenekeepr::examplePedigree)
exampleLoops <- findLoops(exampleTree)

rmsharp/nprcmanager documentation built on April 24, 2021, 3:13 p.m.