nadiv: (Non)Additive Genetic Relatedness Matrices
Version 2.14.3.1

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
URL http://github.com/matthewwolak/nadiv
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nadiv")

Getting started

Package overview
README.md

Popular man pages

aiCI: Confidence Intervals for Variance Components
aiFun: Sampling (co)variances
grfx: Simulated genetic random effects
makeA: Creates the additive genetic relationship matrix
pcc: REML convergence checks
simGG: Genetic group pedigree and data simulation
simPedHS: Half-sib pedigree construction
See all...

All man pages Function index File listing

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

Files

inst
inst/CITATION
src
src/ainv.cc
src/dsim.cc
src/ga.cc
src/cs_multiply.c
src/dfc.cc
src/reT.cc
src/cs_util.c
src/cs_cumsum.c
src/cs_norm.c
src/nadiv.h
src/genedrop.cc
src/cs_malloc.c
src/cs_transpose.c
src/cs.h
src/dij.cc
src/nadivcc.h
src/cs_scatter.c
src/sinv.cc
NAMESPACE
NEWS.md
data
data/Q1988.tab
data/ggTutorial.tab
data/warcolak.tab
data/Mrode2.tab
data/FG90.tab
data/Mrode9.tab
data/F2009.tab
data/Mrode3.tab
data/datalist
R
R/founderLine.R
R/genAssign.R
R/varTrans.R
R/ggcontrib.R
R/simPedDFC.R
R/findDFC.R
R/makeS.R
R/aic.R
R/sm2list.R
R/constrainFun.R
R/plot.proLik.R
R/makeAA.R
R/simPedHS.R
R/numPed.R
R/LRTest.R
R/drfx.R
R/makeDufam.R
R/aiCI.R
R/makeAinv.R
R/makeD.R
R/aiFun.R
R/grfx.R
R/remlSupport.R
R/makeAstarMult.R
R/prunePed.R
R/TDtT.R
R/makeDsim.R
R/parConstrainFun.R
R/proLik.R
R/makeA.R
R/makeDomEpi.R
R/simGG.R
R/prepPed.R
README.md
MD5
DESCRIPTION
man
man/makeAA.Rd
man/ggcontrib.Rd
man/makeDsim.Rd
man/prunePed.Rd
man/sm2list.Rd
man/makeA.Rd
man/drfx.Rd
man/makeD.Rd
man/ggTutorial.Rd
man/varTrans.Rd
man/simGG.Rd
man/FG90.Rd
man/prepPed.Rd
man/aic.Rd
man/numPed.Rd
man/F2009.Rd
man/nadiv-package.Rd
man/Q1988.Rd
man/aiFun.Rd
man/makeAinv.Rd
man/genAssign.Rd
man/pin.Rd
man/makeDomEpi.Rd
man/parConstrainFun.Rd
man/pcc.Rd
man/makeS.Rd
man/simPedDFC.Rd
man/makeAstarMult.Rd
man/warcolak.Rd
man/proLik.Rd
man/Mrode2.Rd
man/grfx.Rd
man/Mrode9.Rd
man/simPedHS.Rd
man/findDFC.Rd
man/aiCI.Rd
man/LRTest.Rd
man/constrainFun.Rd
man/Mrode3.Rd
man/founderLine.Rd
nadiv documentation built on May 20, 2017, 1:34 a.m.

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