# (Non)Additive Genetic Relatedness Matrices

## Documentation for package ‘nadiv’ version 2.17.1

- DESCRIPTION file.

## Help Pages

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
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
pin | Approximate standard errors for linear functions of variance components
plot.proLik | Profile Likelihoods
prepPed | Prepares a pedigree by sorting and adding 'founders'
proLik | 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
_PACKAGE | (Non)Additive Genetic Relatedness Matrices in Animal Model Analyses