⚠️There's a newer version (2.18.0) of this package.Take me there.

nadiv (version 2.11)

Functions to construct non-additive genetic relatedness matrices

Description

Constructs non-additive genetic relationship matrices from a pedigree. These and their inverses can be passed to a linear mixed effect model, known as the 'animal model'.

Copy Link

Version

Install

install.packages('nadiv')

Monthly Downloads

641

Version

2.11

License

GPL (>= 2)

Maintainer

Matthew Wolak

Last Published

February 26th, 2013

Functions in nadiv (2.11)

Mrode9

Pedigree, adapted from example 9.1 of Mrode (2005)

constrainFun

Function used in conjunction with others to produce a profile likelihood for a variance component

makeD

Creates the dominance genetic realationship matrix

proLik

Estimates the profile likelihood of a random effect

plot.proLik

Plot profile Likelihood

parConstrainFun

Function used in the proLik function to produce a profile likelihood for a variance component

FG90

Pedigree, adapted from Table 1 in Fernando & Grossman (1990)

nadiv-package

Functions to create non-additive relationship matrices and their inverses

makeDsim

Creates the dominance genetic relationship matrix through iteration

warcolak

Pedigree and phenotypic values for a mythical population of Warcolaks

sm2list

Converts a sparse matrix into a three column format.

genAssign

Generation assignment

makeS

Creates the additive genetic relationship matrix for the sex chromosomes

numPed

Creates a numeric form of a pedigree

makeDomEpi

Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices

varTrans

Transforms ASReml-R gamma variances to component scale

aiCI

Confidence Intervals for Variance Components

findDFC

Finds the double first cousins in a pedigree

makeAA

Creates the additive by additive epistatic genetic relationship matrix

aiFun

Sampling (co)variances

makeA

Creates the additive genetic relationship matrix

DFC

Indicates Double First Cousins

Mrode2

Pedigree from Table 2.1 of Mrode (2005)