(Non)Additive Genetic Relatedness Matrices

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Documentation for package ‘nadiv’ version 2.17.2

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nadiv-package (Non)Additive Genetic Relatedness Matrices in Animal Model Analyses
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 likelihood for a variance component
drfx Simulated design random effects
F2009 Pedigree adapted from Fikse 2009 with genetic groups and fuzzy classification
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 individual in a pedigree belongs
genAssign Generation assignment
genAssign.default Generation assignment
genAssign.numPed Generation assignment
geneDrop Functions to conduct gene dropping through a pedigree
geneDrop.default Functions to conduct gene dropping through a pedigree
geneDrop.numPed Functions to conduct gene dropping through a pedigree
ggcontrib Genetic group contribution
ggTutorial Simulated dataset used to analyze data with genetic group animal models
grfx Simulated genetic random effects
is.numPed Integer Format Pedigree
is.proLik Profile Likelihoods
LRTest log-Likelihood Ratio Test
makeA Creates the additive genetic relationship matrix
makeAA Creates the additive by additive epistatic genetic relationship matrix
makeAinv Creates the inverse additive genetic relationship matrix
makeAinv.default Creates the inverse additive genetic relationship matrix
makeAinv.fuzzy Creates the inverse additive genetic relationship matrix
makeAstarMult Creates the inverse additive genetic relationship matrix with genetic groups
makeD Create the dominance genetic relationship matrix
makeDiiF Creates components of the additive genetic relationship matrix and its inverse
makeDiiF.default Creates components of the additive genetic relationship matrix and its inverse
makeDiiF.numPed Creates components of the additive genetic relationship matrix and its inverse
makeDomEpi Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices
makeDsim Create the dominance genetic relationship matrix through an iterative (simulation) process
makeGGAinv Creates the inverse additive genetic relationship matrix
makeM Creates the (additive) mutational effects relationship matrix
makeMinv Create the inverse (additive) mutational effects relationship matrix
makeMinvML Create the inverse (additive) mutational effects relationship matrix
makeS Creates the additive genetic relationship matrix for the shared sex chromosomes
makeSd Create the dominance genetic relationship matrix
makeSdsim Create the dominance genetic relationship matrix through an iterative (simulation) process
makeT Creates components of the additive genetic relationship matrix and its inverse
makeT.default Creates components of the additive genetic relationship matrix and its inverse
makeT.numPed Creates components of the additive genetic relationship matrix and its inverse
makeTinv Creates components of the additive genetic relationship matrix and its inverse
makeTinv.default Creates components of the additive genetic relationship matrix and its inverse
makeTinv.numPed Creates components of the additive genetic relationship matrix and its inverse
Mrode2 Pedigree from Table 2.1 of Mrode (2005)
Mrode3 Pedigree, from chapter 3 of Mrode (2005) with genetic groups and a trait column
Mrode9 Pedigree, adapted from example 9.1 of Mrode (2005)
nadiv (Non)Additive Genetic Relatedness Matrices in Animal Model Analyses
numPed Integer Format Pedigree
parConstrainFun Function used in the 'proLik' function to produce a profile likelihood for a variance component
pcc REML convergence checks
plot.proLik Profile Likelihoods
prepPed Prepares a pedigree by sorting and adding 'founders'
proLik Profile Likelihoods
proLik4 Profile Likelihoods
prunePed Prunes a pedigree based on individuals with phenotypes
prunePed.default Prunes a pedigree based on individuals with phenotypes
prunePed.numPed Prunes a pedigree based on individuals with phenotypes
Q1988 Pedigree with genetic groups adapted from Quaas (1988) equation [5]
ronPed Integer Format Pedigree
simGG Genetic group pedigree and data simulation
simPedDFC Double first cousin pedigree construction
simPedHS Half-sib pedigree construction
simPedMCN Middle Class Neighborhood pedigree construction
sm2list Converts a sparse matrix into a three column format.
varTrans Transforms ASReml-R gamma sampling variances to component scale
warcolak Pedigree and phenotypic values for a mythical population of Warcolaks
Wray90 Pedigree, adapted from Wray (1990)
_PACKAGE (Non)Additive Genetic Relatedness Matrices in Animal Model Analyses