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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NEWS

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

Peer review:

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
  • 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]
  • Wray90 - Pedigree, adapted from Wray
  • ggTutorial - Simulated dataset used to analyze data with genetic group animal models
  • warcolak - Pedigree and phenotypic values for a mythical population of Warcolaks

On CRAN:

7.06 score 18 stars 3 packages 142 scripts 780 downloads 12 mentions 41 exports 2 dependencies

Last updated 6 months agofrom:a2d25f23a5. Checks:OK: 3 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-win-x86_64OKOct 25 2024
R-4.5-linux-x86_64OKOct 25 2024
R-4.4-win-x86_64NOTEOct 25 2024
R-4.4-mac-x86_64NOTEOct 25 2024
R-4.4-mac-aarch64NOTEOct 25 2024
R-4.3-win-x86_64NOTEOct 25 2024
R-4.3-mac-x86_64NOTEOct 25 2024
R-4.3-mac-aarch64NOTEOct 25 2024

Exports:aicaiCIaiFunconstrainFundrfxfindDFCfounderLinegenAssigngeneDropggcontribgrfxLRTestmakeAmakeAAmakeAinvmakeAstarMultmakeDmakeDiiFmakeDomEpimakeDsimmakeGGAinvmakeMmakeMinvmakeMinvMLmakeSmakeSdmakeSdsimmakeTmakeTinvnumPedpccpinprepPedprunePedronPedsimGGsimPedDFCsimPedHSsimPedMCNsm2listvarTrans

Dependencies:latticeMatrix

Readme and manuals

Help Manual

Help pageTopics
(Non)Additive Genetic Relatedness Matrices in Animal Model Analysesnadiv-package nadiv
Akaike Information Criterionaic
Confidence Intervals for Variance ComponentsaiCI
Sampling (co)variancesaiFun
Fix a Model Parameter and Conduct Likelihood Ratio TestconstrainFun
Simulated design random effectsdrfx
Pedigree adapted from Fikse 2009 with genetic groups and fuzzy classificationF2009
Pedigree, adapted from Table 1 in Fernando & Grossman (1990)FG90
Finds the double first cousins in a pedigreefindDFC
Identifies the matriline or patriline to which each individual in a pedigree belongsfounderLine
Generation assignmentgenAssign genAssign.default genAssign.numPed
Functions to conduct gene dropping through a pedigreegeneDrop geneDrop.default geneDrop.numPed
Genetic group contributionggcontrib
Simulated dataset used to analyze data with genetic group animal modelsggTutorial
Simulated genetic random effectsgrfx
log-Likelihood Ratio TestLRTest
Creates the additive genetic relationship matrixmakeA
Creates the additive by additive epistatic genetic relationship matrixmakeAA
Creates the inverse additive genetic relationship matrixmakeAinv makeAinv.default makeAinv.fuzzy makeGGAinv
Creates the inverse additive genetic relationship matrix with genetic groupsmakeAstarMult
Create the dominance genetic relationship matrixmakeD makeSd
Creates the additive by dominance and dominance by dominance epistatic genetic relationship matricesmakeDomEpi
Create the dominance genetic relationship matrix through an iterative (simulation) processmakeDsim makeSdsim
Creates the (additive) mutational effects relationship matrixmakeM
Create the inverse (additive) mutational effects relationship matrixmakeMinv makeMinvML
Creates the additive genetic relationship matrix for the shared sex chromosomesmakeS
Creates components of the additive genetic relationship matrix and its inversemakeDiiF 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 columnMrode3
Pedigree, adapted from example 9.1 of Mrode (2005)Mrode9
Integer Format PedigreenumPed ronPed
REML convergence checkspcc
Prepares a pedigree by sorting and adding 'founders'prepPed
Prunes a pedigree based on individuals with phenotypesprunePed prunePed.default prunePed.numPed
Pedigree with genetic groups adapted from Quaas (1988) equation [5]Q1988
Genetic group pedigree and data simulationsimGG
Double first cousin pedigree constructionsimPedDFC
Half-sib pedigree constructionsimPedHS
Middle Class Neighborhood pedigree constructionsimPedMCN
Converts a sparse matrix into a three column format.sm2list
Transforms ASReml-R gamma sampling variances to component scalevarTrans
Pedigree and phenotypic values for a mythical population of Warcolakswarcolak
Pedigree, adapted from Wray (1990)Wray90