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nadiv

R package that 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 for ASReml software.

See the latest developments:

nadiv NEWS page

Overview of main branches:

master branch is the most recent production version (typically the same as what is available from the R CRAN mirrors)
devel branch is a preview of the next release which should be functional and error/bug free, but proceed with caution

To obtain nadiv:

From R:
- see the package page for the latest release of nadiv on CRAN where you can download the source.
- install the latest release of the package directly in R:

   install.packages("nadiv")

- then select your favorite [CRAN mirror](https://CRAN.R-project.org/)

From GitHub:
- clone or download the latest development version here
- install the latest development version directly in R using the remotes package https://github.com/r-lib/remotes:

   library(remotes); install_github("matthewwolak/nadiv", ref = "devel")

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Version

Install

install.packages('nadiv')

Monthly Downloads

719

Version

2.18.0

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/matthewwolak/nadiv

Maintainer

Last Published

May 23rd, 2024

Functions in nadiv (2.18.0)

Akaike Information Criterion

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

Simulated design random effects

Generation assignment

Finds the double first cousins in a pedigree

Genetic group contribution

Functions to conduct gene dropping through a pedigree

Simulated dataset used to analyze data with genetic group animal models

Simulated genetic random effects

Fix a Model Parameter and Conduct Likelihood Ratio Test

Creates the additive genetic relationship matrix

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

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

Creates the (additive) mutational effects relationship matrix

Creates the additive genetic relationship matrix for the shared sex chromosomes

Creates the additive by additive epistatic genetic relationship matrix

Create the dominance genetic relationship matrix

Creates the inverse additive genetic relationship matrix

Creates the inverse additive genetic relationship matrix with genetic groups

Create the inverse (additive) mutational effects relationship matrix

Prepares a pedigree by sorting and adding 'founders'

Prunes a pedigree based on individuals with phenotypes

Double first cousin pedigree construction

(Non)Additive Genetic Relatedness Matrices in Animal Model Analyses

Creates components of the additive genetic relationship matrix and its inverse

Integer Format Pedigree

Genetic group pedigree and data simulation

REML convergence checks

nadiv-deprecated

Deprecated functions in package nadiv.

Approximate standard errors for linear functions of variance components

Pedigree and phenotypic values for a mythical population of Warcolaks

Converts a sparse matrix into a three column format.

Transforms ASReml-R gamma sampling variances to component scale

Middle Class Neighborhood pedigree construction

Half-sib pedigree construction

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

log-Likelihood Ratio Test

Confidence Intervals for Variance Components

Sampling (co)variances

Pedigree, adapted from Wray (1990)

Pedigree from Table 2.1 of Mrode (2005)

Pedigree, from chapter 3 of Mrode (2005) with genetic groups and a trait column

Pedigree adapted from Fikse 2009 with genetic groups and fuzzy classification

Pedigree, adapted from example 9.1 of Mrode (2005)

Pedigree with genetic groups adapted from Quaas (1988) equation [5]