summary.Pedig: Calculates Summary Statistics for Pedigrees.

In optiSel: Optimum Contribution Selection and Population Genetics

Calculates Summary Statistics for Pedigrees.

Description

Calculates summary statistics for pedigrees.

Usage

## S3 method for class 'Pedig'
summary(object, keep.only=NULL, maxd=50, d=4, ...)

Arguments

object	An object from class Pedig, which is usually created with function prePed.
keep.only	The individuals to be included in the summary.
maxd	Maximum pedigree depth.
d	Number of generations taken into account for computing the PCI.
...	further arguments passed to or from other methods

Details

Computes summary statistics for pedigrees, including the numbers of equivalent complete generations, numbers of fully traced generations, numbers of maximum generations traced, indexes of pedigree completeness (MacCluer et al, 1983), and the inbreeding coefficients.

Value

A data frame with the following columns:

Indiv	IDs of the individuals,
equiGen	Number of equivalent complete generations,
fullGen	Number of fully traced generations,
maxGen	Number of maximum generations traced,
PCI	Index of pedigree completeness (MacCluer et al, 1983) in generation d.
Inbreeding	Inbreeding coefficient.

Author(s)

Robin Wellmann

References

MacCluer J W, Boyce A J, Dyke B, Weitkamp L R, Pfenning D W, Parsons C J (1983). Inbreeding and pedigree structure in Standardbred horses. J Hered 74 (6): 394-399.

Examples

data(PedigWithErrors)
Pedig <- prePed(PedigWithErrors)
Summary <- summary(Pedig, keep.only=Pedig$Born %in% (2006:2007))
head(Summary)

hist(Summary$PCI,        xlim=c(0,1),  main="Pedigree Completeness")
hist(Summary$Inbreeding, xlim=c(0,1),  main="Inbreeding")
hist(Summary$equiGen,    xlim=c(0,20), main="Number of Equivalent Complete Generations")
hist(Summary$fullGen,    xlim=c(0,20), main="Number of Fully Traced Generations")
hist(Summary$maxGen,     xlim=c(0,20), main="Number of Maximum Generations Traced")

optiSel documentation built on Sept. 11, 2024, 7:19 p.m.