nadiv2.18.0 package

(Non)Additive Genetic Relatedness Matrices

makeM

Creates the (additive) mutational effects relationship matrix

makeMinv

Create the inverse (additive) mutational effects relationship matrix

makeS

Creates the additive genetic relationship matrix for the shared sex ch...

makeTinv

Creates components of the additive genetic relationship matrix and its...

nadiv-deprecated

Deprecated functions in package nadiv.

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

findDFC

Finds the double first cousins in a pedigree

founderLine

Identifies the matriline or patriline to which each individual in a pe...

genAssign

Generation assignment

geneDrop

Functions to conduct gene dropping through a pedigree

ggcontrib

Genetic group contribution

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

makeAstarMult

Creates the inverse additive genetic relationship matrix with genetic ...

makeD

Create the dominance genetic relationship matrix

makeDomEpi

Creates the additive by dominance and dominance by dominance epistatic...

makeDsim

Create the dominance genetic relationship matrix through an iterative ...

nadiv-package

(Non)Additive Genetic Relatedness Matrices in Animal Model Analyses

numPed

Integer Format Pedigree

pcc

REML convergence checks

pin-deprecated

Approximate standard errors for linear functions of variance component...

prepPed

Prepares a pedigree by sorting and adding 'founders'

prunePed

Prunes a pedigree based on individuals with phenotypes

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

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 (<https://vsni.co.uk/software/asreml>).

  • Maintainer: Matthew Wolak
  • License: GPL (>= 2)
  • Last published: 2024-05-23