makeA

Calculates the the Pedigree-based Additive Relationship Matrix. This is twice the pedigree based kinship matrix.

A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees. The methods are described in:\n Wellmann, R., and Pfeiffer, I. (2009) <doi:10.1017/S0016672309000202>.\n Wellmann, R., and Bennewitz, J. (2011) <doi:10.2527/jas.2010-3709>.\n Wellmann, R., Hartwig, S., Bennewitz, J. (2012) <doi:10.1186/1297-9686-44-34>.\n de Cara, M. A. R., Villanueva, B., Toro, M. A., Fernandez, J. (2013) <doi:10.1111/mec.12560>.\n Wellmann, R., Bennewitz, J., Meuwissen, T.H.E. (2014) <doi:10.1017/S0016672314000196>.\n Wellmann, R. (2019) <doi:10.1186/s12859-018-2450-5>.

Robin Wellmann

optiSel

Optimum Contribution Selection and Population Genetics

makeA function

<dl><dt>Pedig</dt>
<dd>Data frame containing the Pedigree. The data frame has columns (1) Individual, (2) Sire, (3) Dam. Missing parents are coded as NA. Both parents must either be missing or present. If this is not the case use prePed.</dd><dt>keep</dt>
<dd>If <code>keep</code> is provided then kinships are computed only for these animals and their ancestors.</dd><dt>keep.only</dt>
<dd>If <code>keep.only</code> is provided then kinships are computed only for these animals.</dd><dt>AFounder</dt>
<dd>Additive relationship matrix of the founders. The row names are the ids of the founders. By default, founders are assumed to be unrelated. Founders not included in this matrix are also assumed to be unrelated.</dd></dl>

Arguments

Author

Calculates the Pedigree-based Additive Relationship Matrix — makeA

<dl>

<dt>Pedig</dt>
<dd>Data frame containing the Pedigree. The data frame has columns (1) Individual, (2) Sire, (3) Dam. Missing parents are coded as NA. Both parents must either be missing or present. If this is not the case use prePed.</dd>

<dt>keep</dt>
<dd>If <code>keep</code> is provided then kinships are computed only for these animals and their ancestors.</dd>

<dt>keep.only</dt>
<dd>If <code>keep.only</code> is provided then kinships are computed only for these animals.</dd>

<dt>AFounder</dt>
<dd>Additive relationship matrix of the founders. The row names are the ids of the founders. By default, founders are assumed to be unrelated. Founders not included in this matrix are also assumed to be unrelated.</dd>

</dl>

makeA: Calculates the Pedigree-based Additive Relationship Matrix

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