Functions to construct (non)additive genetic relatedness matrices and facilitate animal model analyses

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Documentation for package ‘nadiv’ version 2.12

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nadiv-package Functions to construct (non)additive genetic relatedness matrices and facilitate 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
FG90 Pedigree, adapted from Table 1 in Fernando & Grossman (1990)
findDFC Finds the double first cousins in a pedigree
genAssign Generation assignment
grfx Simulated genetic random effects
makeA Creates the additive genetic relationship matrix
makeAA Creates the additive by additive epistatic genetic relationship matrix
makeD Creates the dominance genetic realationship matrix
makeDomEpi Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices
makeDsim Creates the dominance genetic relationship matrix through an iterative (simulation) process
makeS Creates the additive genetic relationship matrix for the shared sex chromosomes
Mrode2 Pedigree from Table 2.1 of Mrode (2005)
Mrode9 Pedigree, adapted from example 9.1 of Mrode (2005)
nadiv Functions to construct (non)additive genetic relatedness matrices and facilitate animal model analyses
numPed Creates a numeric form of a pedigree
parConstrainFun Function used in the 'proLik' function to produce a profile likelihood for a variance component
plot Plot profile Likelihood
plot.proLik Plot profile Likelihood
proLik Estimates the profile likelihood of a random effect
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 variances to component scale
warcolak Pedigree and phenotypic values for a mythical population of Warcolaks