nadiv: (Non)Additive Genetic Relatedness Matrices

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).

AuthorMatthew Wolak [cre, aut]
Date of publication2016-09-22 22:49:49
MaintainerMatthew Wolak <matthewwolak@gmail.com>
LicenseGPL (>= 2)
Version2.14.3.1
http://github.com/matthewwolak/nadiv

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...

Functions

aic Man page
aiCI Man page
aiFun Man page
constrainFun Man page
drfx Man page
F2009 Man page
FG90 Man page
findDFC Man page
founderLine Man page
genAssign Man page
ggcontrib Man page
ggTutorial Man page
grfx Man page
is.numPed Man page
is.proLik Man page
LRTest Man page
makeA Man page
makeAA Man page
makeAinv Man page
makeAinv.default Man page
makeAinv.fuzzy Man page
makeAstarMult Man page
makeD Man page
makeDomEpi Man page
makeDsim Man page
makeS Man page
Mrode2 Man page
Mrode3 Man page
Mrode9 Man page
nadiv Man page
nadiv-package Man page
numPed Man page
parConstrainFun Man page
pcc Man page
pin Man page
plot.proLik Man page
prepPed Man page
proLik Man page
prunePed Man page
Q1988 Man page
ronPed Man page
simGG Man page
simPedDFC Man page
simPedHS Man page
sm2list Man page
varTrans Man page
warcolak Man page

Files

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

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