nadiv: (Non)Additive Genetic Relatedness Matrices

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Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (http://www.vsni.co.uk/software/asreml).

Author
Matthew Wolak [cre, aut]
Date of publication
2016-09-22 22:49:49
Maintainer
Matthew Wolak <matthewwolak@gmail.com>
License
GPL (>= 2)
Version
2.14.3.1
URLs

View on CRAN

Man pages

aic
Akaike Information Criterion
aiCI
Confidence Intervals for Variance Components
aiFun
Sampling (co)variances
constrainFun
Function used in conjunction with others to produce a profile...
drfx
Simulated design random effects
F2009
Pedigree, adapted from Fikse (2009)
FG90
Pedigree, adapted from Table 1 in Fernando & Grossman (1990)
findDFC
Finds the double first cousins in a pedigree
founderLine
Identifies the matriline or patriline to which each...
genAssign
Generation assignment
ggcontrib
Genetic group contribution
ggTutorial
Simulated dataset used to analyze data with genetic group...
grfx
Simulated genetic random effects
LRTest
log-Likelihood Ratio Test
makeA
Creates the additive genetic relationship matrix
makeAA
Creates the additive by additive epistatic genetic...
makeAinv
Creates the inverse additive genetic relationship matrix
makeAstarMult
Creates the inverse additive genetic relationship matrix with...
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 an...
makeS
Creates the additive genetic relationship matrix for the...
Mrode2
Pedigree from Table 2.1 of Mrode (2005)
Mrode3
Pedigree, from chapter 3 of Mrode (2005)
Mrode9
Pedigree, adapted from example 9.1 of Mrode (2005)
nadiv-package
(Non)Additive Genetic Relatedness Matrices in Animal Model...
numPed
Integer Format Pedigree
parConstrainFun
Function used in the 'proLik' function to produce a profile...
pcc
REML convergence checks
pin
Approximate standard errors for linear functions of variance...
prepPed
Prepares a pedigree by sorting and adding 'founders'
proLik
Profile Likelihoods
prunePed
Prunes a pedigree based on individuals with phenotypes
Q1988
Pedigree, adapted from Quaas (1988) equation [5]
simGG
Genetic group pedigree and data simulation
simPedDFC
Double first cousin pedigree construction
simPedHS
Half-sib pedigree construction
sm2list
Converts a sparse matrix into a three column format.
varTrans
Transforms ASReml-R gamma sampling variances to component...
warcolak
Pedigree and phenotypic values for a mythical population of...

Files in this package

nadiv
nadiv/inst
nadiv/inst/CITATION
nadiv/src
nadiv/src/ainv.cc
nadiv/src/dsim.cc
nadiv/src/ga.cc
nadiv/src/cs_multiply.c
nadiv/src/dfc.cc
nadiv/src/reT.cc
nadiv/src/cs_util.c
nadiv/src/cs_cumsum.c
nadiv/src/cs_norm.c
nadiv/src/nadiv.h
nadiv/src/genedrop.cc
nadiv/src/cs_malloc.c
nadiv/src/cs_transpose.c
nadiv/src/cs.h
nadiv/src/dij.cc
nadiv/src/nadivcc.h
nadiv/src/cs_scatter.c
nadiv/src/sinv.cc
nadiv/NAMESPACE
nadiv/NEWS.md
nadiv/data
nadiv/data/Q1988.tab
nadiv/data/ggTutorial.tab
nadiv/data/warcolak.tab
nadiv/data/Mrode2.tab
nadiv/data/FG90.tab
nadiv/data/Mrode9.tab
nadiv/data/F2009.tab
nadiv/data/Mrode3.tab
nadiv/data/datalist
nadiv/R
nadiv/R/founderLine.R
nadiv/R/genAssign.R
nadiv/R/varTrans.R
nadiv/R/ggcontrib.R
nadiv/R/simPedDFC.R
nadiv/R/findDFC.R
nadiv/R/makeS.R
nadiv/R/aic.R
nadiv/R/sm2list.R
nadiv/R/constrainFun.R
nadiv/R/plot.proLik.R
nadiv/R/makeAA.R
nadiv/R/simPedHS.R
nadiv/R/numPed.R
nadiv/R/LRTest.R
nadiv/R/drfx.R
nadiv/R/makeDufam.R
nadiv/R/aiCI.R
nadiv/R/makeAinv.R
nadiv/R/makeD.R
nadiv/R/aiFun.R
nadiv/R/grfx.R
nadiv/R/remlSupport.R
nadiv/R/makeAstarMult.R
nadiv/R/prunePed.R
nadiv/R/TDtT.R
nadiv/R/makeDsim.R
nadiv/R/parConstrainFun.R
nadiv/R/proLik.R
nadiv/R/makeA.R
nadiv/R/makeDomEpi.R
nadiv/R/simGG.R
nadiv/R/prepPed.R
nadiv/README.md
nadiv/MD5
nadiv/DESCRIPTION
nadiv/man
nadiv/man/makeAA.Rd
nadiv/man/ggcontrib.Rd
nadiv/man/makeDsim.Rd
nadiv/man/prunePed.Rd
nadiv/man/sm2list.Rd
nadiv/man/makeA.Rd
nadiv/man/drfx.Rd
nadiv/man/makeD.Rd
nadiv/man/ggTutorial.Rd
nadiv/man/varTrans.Rd
nadiv/man/simGG.Rd
nadiv/man/FG90.Rd
nadiv/man/prepPed.Rd
nadiv/man/aic.Rd
nadiv/man/numPed.Rd
nadiv/man/F2009.Rd
nadiv/man/nadiv-package.Rd
nadiv/man/Q1988.Rd
nadiv/man/aiFun.Rd
nadiv/man/makeAinv.Rd
nadiv/man/genAssign.Rd
nadiv/man/pin.Rd
nadiv/man/makeDomEpi.Rd
nadiv/man/parConstrainFun.Rd
nadiv/man/pcc.Rd
nadiv/man/makeS.Rd
nadiv/man/simPedDFC.Rd
nadiv/man/makeAstarMult.Rd
nadiv/man/warcolak.Rd
nadiv/man/proLik.Rd
nadiv/man/Mrode2.Rd
nadiv/man/grfx.Rd
nadiv/man/Mrode9.Rd
nadiv/man/simPedHS.Rd
nadiv/man/findDFC.Rd
nadiv/man/aiCI.Rd
nadiv/man/LRTest.Rd
nadiv/man/constrainFun.Rd
nadiv/man/Mrode3.Rd
nadiv/man/founderLine.Rd