summary.Pedig: Calculates Summary Statistics for Pedigrees.

In optiSel: Optimum Contribution Selection and Population Genetics

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")

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Pedigree loops were detected. We recommend to correct them manually before
using prePed(). The parents of the following individuals are set to unknown
to remove the loops.
                           Sire             Dam
276000802875148 276000803622423 276000890878480
276000811476506 276000810087663 276000811476506

The sex of the following animals was not compatible with the pedigree, so
it was modified:
                           Sire             Dam
276000810087663 276000802940621 276000802925028

                          Indiv equiGen fullGen maxGen PCI Inbreeding
276000891875979 276000891875979     0.5       0      1   0          0
276000891967895 276000891967895     0.5       0      1   0          0
276000891955445 276000891955445     0.5       0      1   0          0
276000892056808 276000892056808     0.5       0      1   0          0
276000891492096 276000891492096     0.5       0      1   0          0
276000892145644 276000892145644     0.5       0      1   0          0

optiSel documentation built on March 13, 2020, 3:09 a.m.