sampleIndiv

Sampling Individuals from a Pedigree.

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

sampleIndiv function

<dl><dt>Pedig</dt>
<dd>Pedigree with column <code>Indiv</code> and the column specified in parameter <code>from</code>.</dd><dt>from</dt>
<dd>Column name. From each cohort specified in this column (e.g. year of birth), the number of individuals specified in parameter <code>each</code> is sampled. If a cohort contains less individuals, then all individuals are chosen.</dd><dt>each</dt>
<dd>Number of individuals to be sampled from each cohort.</dd></dl>

Arguments

Author

Sample Individuals from Pedigree — sampleIndiv

<dl>

<dt>Pedig</dt>
<dd>Pedigree with column <code>Indiv</code> and the column specified in parameter <code>from</code>.</dd>

<dt>from</dt>
<dd>Column name. From each cohort specified in this column (e.g. year of birth), the number of individuals specified in parameter <code>each</code> is sampled. If a cohort contains less individuals, then all individuals are chosen.</dd>

<dt>each</dt>
<dd>Number of individuals to be sampled from each cohort.</dd>

</dl>

sampleIndiv: Sample Individuals from Pedigree

Description

Usage

Value

Arguments

Author

Details

Examples