nadiv: Functions to construct non-additive genetic relatedness matrices
Version 2.8

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'.

AuthorMatthew Wolak
Date of publicationNone
MaintainerMatthew Wolak <matthewwolak@gmail.com>
LicenseGPL (>=2)
Version2.8
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nadiv", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

constrainFun: Function used in the 'proLik' function to produce a profile...
DFC: Indicates Double First Cousins
genAssign: Generation assignment
IBD: Identical by descent
makeA: Creates the additive genetic relationship matrix
makeD: Creates the dominance genetic realationship matrix
Mrode2: Pedigree from Table 2.1 of Mrode (2005)
See all...

All man pages Function index File listing

Man pages

aiFun: Sampling (co)variances and correlations
choose: Internal function for 'makeDsim'
constrainFun: Function used in the 'proLik' function to produce a profile...
DFC: Indicates Double First Cousins
findBetween: Determines how close estimates are to a true value
findDFC: Finds the double first cousins in a pedigree
genAssign: Generation assignment
IBD: Identical by descent
IBD2: Identity by descent helper function
makeA: Creates the additive genetic relationship matrix
makeAA: Creates the additive by additive epistatic genetic...
makeD: Creates the dominance genetic realationship matrix
makeDomEpi: Creates the additive by dominance and dominance by dominance...
makeDsim: Creates the dominance genetic relationship matrix through...
Mrode2: Pedigree from Table 2.1 of Mrode (2005)
Mrode9: Pedigree, adapted from example 9.1 of Mrode (2005)
nadiv-package: Functions to create non-additive relationship matrices and...
numPed: Creates a numeric form of a pedigree
plot.proLik: Graphically depicts the profile Likelihood
proLik: Estimates the profile likelihood of a random effect
SEfun: Estimate of the standard error for a simulated coefficient of...
sm2list: Converts a sparse matrix into a three column format.
vchoose: Helper function for another internal function in 'makeDsim'
warcolak: Pedigree and phenotypic values for a mythical population of...

Functions

DFC Man page Source code
IBD Man page Source code
IBD2 Man page Source code
LRTest Source code
Mrode2 Man page
Mrode9 Man page
SEfun Man page Source code
aiFun Man page Source code
choose Man page Source code
constrainFun Man page Source code
findBetween Man page Source code
findDFC Man page Source code
genAssign Man page Source code
makeA Man page Source code
makeAA Man page Source code
makeD Man page Source code
makeDomEpi Man page Source code
makeDsim Man page Source code
nadiv Man page
nadiv-package Man page
numPed Man page Source code
plot Man page
plot.proLik Man page Source code
proLik Man page Source code
sm2list Man page Source code
vchoose Man page Source code
warcolak Man page

Files

data
data/warcolak.tab.gz
data/Mrode9.tab.gz
data/Mrode2.tab.gz
R
R/IBD2.R
R/aiFun.R
R/SEfun.R
R/DFC.R
R/sm2list.R
R/makeD.R
R/vchoose.R
R/findBetween.R
R/constrainFun.R
R/makeAA.R
R/plot.proLik.R
R/makeA.R
R/LRTest.R
R/choose.R
R/findDFC.R
R/genAssign.R
R/numPed.R
R/IBD.R
R/makeDsim.R
R/proLik.R
R/makeDomEpi.R
NAMESPACE
inst
inst/CITATION
DESCRIPTION
man
man/DFC.Rd
man/proLik.Rd
man/plot.proLik.Rd
man/warcolak.Rd
man/findBetween.Rd
man/makeA.Rd
man/sm2list.Rd
man/Mrode9.Rd
man/SEfun.Rd
man/IBD.Rd
man/nadiv-package.Rd
man/choose.Rd
man/findDFC.Rd
man/vchoose.Rd
man/aiFun.Rd
man/Mrode2.Rd
man/numPed.Rd
man/makeAA.Rd
man/makeDomEpi.Rd
man/IBD2.Rd
man/makeD.Rd
man/constrainFun.Rd
man/genAssign.Rd
man/makeDsim.Rd
src
src/dij.f90
nadiv documentation built on May 21, 2017, 12:52 a.m.

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