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nadiv (version 2.14.2)

(Non)Additive Genetic Relatedness Matrices

Description

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 (http://www.vsni.co.uk/software/asreml).

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install.packages('nadiv')

Monthly Downloads

1,601

Version

2.14.2

License

GPL (>= 2)

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Repository

http://github.com/matthewwolak/nadiv

Maintainer

Matthew Wolak

Last Published

February 5th, 2016

Functions in nadiv (2.14.2)

Pedigree from Table 2.1 of Mrode (2005)

Integer Format Pedigree

Simulated design random effects

Creates the additive genetic relationship matrix for the shared sex chromosomes

Function used in conjunction with others to produce a profile likelihood for a variance component

Akaike Information Criterion

Profile Likelihoods

parConstrainFun

Function used in the proLik function to produce a profile likelihood for a variance component

Sampling (co)variances

Creates the dominance genetic realationship matrix

Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices

Creates the additive by additive epistatic genetic relationship matrix

Generation assignment

Approximate standard errors for linear functions of variance components

(Non)Additive Genetic Relatedness Matrices in Animal Model Analyses

Confidence Intervals for Variance Components

Pedigree, from chapter 3 of Mrode (2005)

Creates the inverse additive genetic relationship matrix

REML convergence checks

Converts a sparse matrix into a three column format.

Simulated genetic random effects

Creates the additive genetic relationship matrix

Double first cousin pedigree construction

Creates the dominance genetic relationship matrix through an iterative (simulation) process

Pedigree, adapted from Quaas (1988) equation [5]

Finds the double first cousins in a pedigree

Half-sib pedigree construction

Transforms ASReml-R gamma variances to component scale

Pedigree and phenotypic values for a mythical population of Warcolaks

Genetic group contribution

Prunes a pedigree based on individuals with phenotypes

Prepares a pedigree by sorting and adding 'founders'

Pedigree, adapted from example 9.1 of Mrode (2005)

Identifies the matriline or patriline to which each individual in a pedigree belongs

Pedigree, adapted from Table 1 in Fernando & Grossman (1990)