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nadiv (version 2.9)

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

2.9

License

GPL (>= 2)

Maintainer

Matthew Wolak

Last Published

March 28th, 2012

Functions in nadiv (2.9)

aiCI

Confidence Intervals for Variance Components
numPed

Creates a numeric form of a pedigree
vchoose

Helper function for another internal function in makeDsim
genAssign

Generation assignment
IBD

Identical by descent
Mrode2

Pedigree from Table 2.1 of Mrode (2005)
chooser

Internal function for makeDsim
warcolak

Pedigree and phenotypic values for a mythical population of Warcolaks
parConstrainFun

Function used in the proLik function to produce a profile likelihood for a variance component
Mrode9

Pedigree, adapted from example 9.1 of Mrode (2005)
IBD2

Identity by descent helper function
sm2list

Converts a sparse matrix into a three column format.
makeAA

Creates the additive by additive epistatic genetic relationship matrix
makeD

Creates the dominance genetic realationship matrix
wrap_dij

Wrapper function for makeD
varTrans

Transforms ASReml-R gamma variances to component scale
nadiv-package

Functions to create non-additive relationship matrices and their inverses
findBetween

Determines how close estimates are to a true value
DFC

Indicates Double First Cousins
SEfun

Estimate of the standard error for a simulated coefficient of fraternity
makeDsim

Creates the dominance genetic relationship matrix through iteration
aiFun

Sampling (co)variances and correlations
makeDomEpi

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

Double First Cousin wrapper function
proLik

Estimates the profile likelihood of a random effect
plot.proLik

Plot profile Likelihood
makeA

Creates the additive genetic relationship matrix
findDFC

Finds the double first cousins in a pedigree
constrainFun

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