ped_clean

Remove individuals that are not necessary for purging analyses involving fitness.
This will reduce the size of the pedigree, and speed up the computation of inbreeding
parameters.
Individuals removed include those with unknown (NA)
values of a given parameter, as long as they do not have any descendant in the
pedigree with known values of that parameter.
Cleaned pedigrees will automatically have individual identities
renamed (see <code>ped_rename</code>).

Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.

Eugenio L<c3><b3>pez-Cortegano

purgeR

Inbreeding-Purging Estimation in Pedigreed Populations

Eugenio López-Cortegano

ped_clean function

<dl><dt>ped</dt>
<dd>A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.</dd>
<dt>value_from</dt>
<dd>Name of the column of interest.</dd></dl>

Arguments

Remove individuals not used for purging analyses — ped_clean

<dl>

<dt>ped</dt>
<dd>A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.</dd>


<dt>value_from</dt>
<dd>Name of the column of interest.</dd>

</dl>

ped_clean: Remove individuals not used for purging analyses

Description

Usage

Value

Arguments

See Also

Examples