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...

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

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