Package: nadiv 2.18.0

nadiv: (Non)Additive Genetic Relatedness Matrices

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>).

Authors:Matthew Wolak [cre, aut]

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manual.pdf |manual.html✨
card.svg |card.png
nadiv/json (API)
NEWS

# Install 'nadiv' in R:

install.packages('nadiv', repos = c('https://matthewwolak.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/matthewwolak/nadiv/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

F2009 - Pedigree adapted from Fikse 2009 with genetic groups and fuzzy classification
FG90 - Pedigree, adapted from Table 1 in Fernando & Grossman
ggTutorial - Simulated dataset used to analyze data with genetic group animal models
Mrode2 - Pedigree from Table 2.1 of Mrode
Mrode3 - Pedigree, from chapter 3 of Mrode (2005) with genetic groups and a trait column
Mrode9 - Pedigree, adapted from example 9.1 of Mrode
Q1988 - Pedigree with genetic groups adapted from Quaas (1988) equation [5]
warcolak - Pedigree and phenotypic values for a mythical population of Warcolaks
Wray90 - Pedigree, adapted from Wray

On CRAN:

cpp

7.44 score 23 stars 3 packages 202 scripts 1.3k downloads 12 mentions 41 exports 2 dependencies

Last updated from:a2d25f23a5. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	141
linux-devel-x86_64	OK	134
source / vignettes	OK	166
linux-release-arm64	OK	125
linux-release-x86_64	OK	127
macos-release-arm64	OK	185
macos-release-x86_64	OK	289
macos-oldrel-arm64	OK	227
macos-oldrel-x86_64	OK	266
windows-devel	OK	120
windows-release	OK	114
windows-oldrel	OK	127
wasm-release	OK	106

Exports:aic aiCI aiFun constrainFun drfx findDFC founderLine genAssign geneDrop ggcontrib grfx LRTest makeA makeAA makeAinv makeAstarMult makeD makeDiiF makeDomEpi makeDsim makeGGAinv makeM makeMinv makeMinvML makeS makeSd makeSdsim makeT makeTinv numPed pcc pin prepPed prunePed ronPed simGG simPedDFC simPedHS simPedMCN sm2list varTrans

Dependencies:lattice Matrix

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
(Non)Additive Genetic Relatedness Matrices in Animal Model Analyses	nadiv-package nadiv
Akaike Information Criterion	aic
Confidence Intervals for Variance Components	aiCI
Sampling (co)variances	aiFun
Fix a Model Parameter and Conduct Likelihood Ratio Test	constrainFun
Simulated design random effects	drfx
Pedigree adapted from Fikse 2009 with genetic groups and fuzzy classification	F2009
Pedigree, adapted from Table 1 in Fernando & Grossman (1990)	FG90
Finds the double first cousins in a pedigree	findDFC
Identifies the matriline or patriline to which each individual in a pedigree belongs	founderLine
Generation assignment	genAssign genAssign.default genAssign.numPed
Functions to conduct gene dropping through a pedigree	geneDrop geneDrop.default geneDrop.numPed
Genetic group contribution	ggcontrib
Simulated dataset used to analyze data with genetic group animal models	ggTutorial
Simulated genetic random effects	grfx
log-Likelihood Ratio Test	LRTest
Creates the additive genetic relationship matrix	makeA
Creates the additive by additive epistatic genetic relationship matrix	makeAA
Creates the inverse additive genetic relationship matrix	makeAinv makeAinv.default makeAinv.fuzzy makeGGAinv
Creates the inverse additive genetic relationship matrix with genetic groups	makeAstarMult
Create the dominance genetic relationship matrix	makeD makeSd
Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices	makeDomEpi
Create the dominance genetic relationship matrix through an iterative (simulation) process	makeDsim makeSdsim
Creates the (additive) mutational effects relationship matrix	makeM
Create the inverse (additive) mutational effects relationship matrix	makeMinv makeMinvML
Creates the additive genetic relationship matrix for the shared sex chromosomes	makeS
Creates components of the additive genetic relationship matrix and its inverse	makeDiiF makeDiiF.default makeDiiF.numPed makeT makeT.default makeT.numPed makeTinv makeTinv.default makeTinv.numPed
Pedigree from Table 2.1 of Mrode (2005)	Mrode2
Pedigree, from chapter 3 of Mrode (2005) with genetic groups and a trait column	Mrode3
Pedigree, adapted from example 9.1 of Mrode (2005)	Mrode9
Integer Format Pedigree	numPed ronPed
REML convergence checks	pcc
Prepares a pedigree by sorting and adding 'founders'	prepPed
Prunes a pedigree based on individuals with phenotypes	prunePed prunePed.default prunePed.numPed
Pedigree with genetic groups adapted from Quaas (1988) equation [5]	Q1988
Genetic group pedigree and data simulation	simGG
Double first cousin pedigree construction	simPedDFC
Half-sib pedigree construction	simPedHS
Middle Class Neighborhood pedigree construction	simPedMCN
Converts a sparse matrix into a three column format.	sm2list
Transforms ASReml-R gamma sampling variances to component scale	varTrans
Pedigree and phenotypic values for a mythical population of Warcolaks	warcolak
Pedigree, adapted from Wray (1990)	Wray90