optiSel (version 0.9.1)

summary.kinMatrices: Calculates Genetic Parameters for Age Cohorts

Description

Computes for every age cohort several genetic parameters. These are average kinships, gene diversity at native loci, native effective size, and native genome equivalents.

Usage

# S3 method for kinMatrices
summary(object, Pedig, tlim=NULL, histNe=NULL, base=NULL, df=4, ...)

Arguments

object

This is typically the output of function kinlist. A named list containing kinship matrices of the individuals to be used for computing mean kinships. Typically individuals from different age cohorts are included, but only from the breed of interest.

Pedig

Data frame containing the Pedigree. The data frame has columns (1) Individual, (2) Sire, (3) Dam, and column Born containing for every individual the age cohort to which it belongs (typically year of birth).

tlim

Numeric vector with 2 components giving the time span for which genetic parameters are to be computed.

histNe

The historic effective size of the population assumed for the time before tlim[1]. The default is 3 times the average native effective size within the time span of interest. This parameter is needed only for computing the conditional gene diversity and the native genome equivalents.

base

The base year in which individuals are assumed to be unrelated. The default is 25 generations before tlim[1]. This parameter is needed only for computing the conditional gene diversity and the native genome equivalents.

df

Smoothing parameter used for computing the native effective size. The default is df=4.

...

further arguments passed to or from other methods

Value

A data frame providing for every age cohort (some of) the genetic parameters mentioned above.

Details

This function computes for every age cohort several genetic parameters. These may include

pedIBD	The average pedigree based kinship within the age cohort.
pedIBDorM	The probability that 2 alleles chosen from the age cohort are
	IBD or that at least one of them originates from a migrant.
pedIBDorMM	The probability that 2 alleles chosen from the age cohort are
	IBD or that both of them are from migrants.
pedIBDofN	The conditional probability that 2 alleles chosen from the
	age cohort are IBD, given that both are from native founders.
condGD	The diversity at native alleles, i.e. the conditional probability
	that 2 alleles chosen from the age cohort are not IBD, given that
	both are from native founders. Individuals born in the base-year
	are assumed to be unrelated.
Ne	The native effective size, quantifying how fast the diversity at native
	alleles is decreasing. The diversity may increase for a short time
	span, in which case the estimate would be NA. Use a smaller value
	for parameter df to get a smooth estimate.
NGE	The native genome equivalents. The parameter estimates the number of
	unrelated individuals that would be needed to establish a hypothetical
	new population that has the same condGD as the population under
	study. Individuals born in the base-year are assumed to be unrelated.

Examples

# NOT RUN {
data(ExamplePed)
Pedig    <- prePed(ExamplePed, thisBreed="Hinterwaelder", lastNative=1970)
Kinships <- kinlist(pedIBD=pedIBD(Pedig), pedIBDatN=pedIBDatN(Pedig, thisBreed="Hinterwaelder"))
summary(Kinships, Pedig, tlim=c(1970,2005), histNe=150, base=1800)
# }