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nadiv (version 2.8)

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'.

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Version

Install

install.packages('nadiv')

Monthly Downloads

641

Version

2.8

License

GPL (>= 2)

Maintainer

Matthew Wolak

Last Published

February 7th, 2012

Functions in nadiv (2.8)

findDFC

Finds the double first cousins in a pedigree

genAssign

Generation assignment

Mrode2

Pedigree from Table 2.1 of Mrode (2005)

warcolak

Pedigree and phenotypic values for a mythical population of Warcolaks

proLik

Estimates the profile likelihood of a random effect

makeDsim

Creates the dominance genetic relationship matrix through simulation

DFC

Indicates Double First Cousins

makeD

Creates the dominance genetic realationship matrix

vchoose

Helper function for another internal function in makeDsim

numPed

Creates a numeric form of a pedigree

SEfun

Estimate of the standard error for a simulated coefficient of fraternity

constrainFun

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

nadiv-package

Functions to create non-additive relationship matrices and their inverses

sm2list

Converts a sparse matrix into a three column format.

Mrode9

Pedigree, adapted from example 9.1 of Mrode (2005)

IBD2

Identity by descent helper function

findBetween

Determines how close estimates are to a true value

makeA

Creates the additive genetic relationship matrix

plot.proLik

Graphically depicts the profile Likelihood

IBD

Identical by descent

makeAA

Creates the additive by additive epistatic genetic relationship matrix

aiFun

Sampling (co)variances and correlations

makeDomEpi

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

choose

Internal function for makeDsim