makeAA
(Package: nadiv) :
Creates the additive by additive epistatic genetic relationship matrix
Given a pedigree, the matrix of additive by additive genetic relatedness (AA) among all individuals in the pedigree is returned.
● Data Source:
CranContrib
● Keywords:
● Alias: makeAA
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Calculates the genomic contribution each genetic group makes to every individual in a pedigree
● Data Source:
CranContrib
● Keywords:
● Alias: ggcontrib
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Alleles are explicitly traced through a pedigree to obtain coefficients of fraternity between pairs of individuals (the probability of sharing both alleles identical by descent). This is accomplished in an iterative process to account for the various routes by which an allele will progress through a pedigree due to Mendelian sampling. This is an implementation of the simulation approach of Ovaskainen et al. (2008).
● Data Source:
CranContrib
● Keywords:
● Alias: makeDsim
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prunePed
(Package: nadiv) :
Prunes a pedigree based on individuals with phenotypes
This function removes individuals who are either not themselves or not ancestors to phenotyped individuals
● Data Source:
CranContrib
● Keywords:
● Alias: prunePed
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sm2list
(Package: nadiv) :
Converts a sparse matrix into a three column format.
From a sparse matrix object, the three column, row ordered lower triangle of non-zero elements is created. Mostly used within other functions (i.e., makeD)
● Data Source:
CranContrib
● Keywords:
● Alias: sm2list
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makeA
(Package: nadiv) :
Creates the additive genetic relationship matrix
This returns the additive relationship matrix in sparse matrix format.
● Data Source:
CranContrib
● Keywords:
● Alias: makeA
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This function simulates effects for random terms in a linear mixed model based on design matrices. The intended purpose is for simulating environmental effects from a pedigree.
● Data Source:
CranContrib
● Keywords:
● Alias: drfx
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makeD
(Package: nadiv) :
Creates the dominance genetic realationship matrix
Given a pedigree, the matrix of coefficients of fraternity are returned - the D matrix. Note, inbreeding is not directly incorporated into the calculation of the coefficients (see Details). Will return the inverse of the D matrix by default, otherwise this operation can be skipped if desired.
● Data Source:
CranContrib
● Keywords:
● Alias: makeD
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The inverse of the Average Information matrix in an ASReml-R object produces the sampling variances of the random effects on the gamma scale. This function scales these variances to the original component scale. This allows for Confidence Intervals to be constructed about the variance component estimates.
● Data Source:
CranContrib
● Keywords:
● Alias: varTrans
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Simulates a pedigree and phenotype for a focal population receiving immigrants. Genetic and environmental differences can be specified between the focal and immigrant populations. Further, these differences can have temporal trends.
● Data Source:
CranContrib
● Keywords:
● Alias: simGG
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providing 
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