nadiv: Functions to construct non-additive genetic relatedness matrices

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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'.

Author
Matthew Wolak
Date of publication
None
Maintainer
Matthew Wolak <matthewwolak@gmail.com>
License
GPL (>=2)
Version
2.8

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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...

Files in this package

nadiv
nadiv/data
nadiv/data/warcolak.tab.gz
nadiv/data/Mrode9.tab.gz
nadiv/data/Mrode2.tab.gz
nadiv/R
nadiv/R/IBD2.R
nadiv/R/aiFun.R
nadiv/R/SEfun.R
nadiv/R/DFC.R
nadiv/R/sm2list.R
nadiv/R/makeD.R
nadiv/R/vchoose.R
nadiv/R/findBetween.R
nadiv/R/constrainFun.R
nadiv/R/makeAA.R
nadiv/R/plot.proLik.R
nadiv/R/makeA.R
nadiv/R/LRTest.R
nadiv/R/choose.R
nadiv/R/findDFC.R
nadiv/R/genAssign.R
nadiv/R/numPed.R
nadiv/R/IBD.R
nadiv/R/makeDsim.R
nadiv/R/proLik.R
nadiv/R/makeDomEpi.R
nadiv/NAMESPACE
nadiv/inst
nadiv/inst/CITATION
nadiv/DESCRIPTION
nadiv/man
nadiv/man/DFC.Rd
nadiv/man/proLik.Rd
nadiv/man/plot.proLik.Rd
nadiv/man/warcolak.Rd
nadiv/man/findBetween.Rd
nadiv/man/makeA.Rd
nadiv/man/sm2list.Rd
nadiv/man/Mrode9.Rd
nadiv/man/SEfun.Rd
nadiv/man/IBD.Rd
nadiv/man/nadiv-package.Rd
nadiv/man/choose.Rd
nadiv/man/findDFC.Rd
nadiv/man/vchoose.Rd
nadiv/man/aiFun.Rd
nadiv/man/Mrode2.Rd
nadiv/man/numPed.Rd
nadiv/man/makeAA.Rd
nadiv/man/makeDomEpi.Rd
nadiv/man/IBD2.Rd
nadiv/man/makeD.Rd
nadiv/man/constrainFun.Rd
nadiv/man/genAssign.Rd
nadiv/man/makeDsim.Rd
nadiv/src
nadiv/src/dij.f90