(Non)Additive Genetic Relatedness Matrices

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Documentation for package ‘nadiv’ version 2.18.0

• DESCRIPTION file.
• Package NEWS.

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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	Fix a Model Parameter and Conduct Likelihood Ratio Test
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
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
pcc	REML convergence checks
prepPed	Prepares a pedigree by sorting and adding 'founders'
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)