AlphaPart (version 0.9.7)

summary.AlphaPart: A function to summarize AlphaPart object.

Description

Breedng values of individuals are often summarized, either by year of birth or some other classification. Function summary.AlphaPart provides a way to ease the computation of such summaries on partitions of breeding values.

Usage

# S3 method for AlphaPart
summary(object, by, FUN, labelSum, subset,
  sums, cov,  ...)

Value

An object of class summaryAlphaPart, which is a list of data frames with summary statistics on breeding value partitions. For each trait there a dataframe holds summary for the "whole/original" breeding value and its partitions. In addition another list is added (named info) with the following components holdinfg meta info:

path

column name holding path information

nP

number of paths

lP

path labels

nT

number of traits

lT

trait labels

by

column name of variable by which summary was performed

warn

potential warning messages associated with this object

labelSum

column name of summary for "whole/original" breeding values

There is a handy plot method (plot.summaryAlphaPart) for output.

Arguments

object

AlphaPart, output object from AlphaPart function.

by

Character, the name of a column by which summary function FUN should be applied; if NULL (default) summary is given for the whole table.

FUN

Function, which function should be used in summary; function should return single value per each level of by.

labelSum

Character, label used for the overall breeding value.

subset

Logical, perform summary only on a subset of object subsetted by this argument.

sums

Logical, link between AlphaPart and summary.AlphaPart() (only for internal use!).

cov

Logical, if FALSE returns n variances plus one additional column containing two times the sum of all covariances; otherwise returns n variance and n(n-1)/2 covariances in the form of 2*Cov(., .), where n is the number of partitions. This argument only works when FUN = var. Defaut cov = FALSE.

...

Arguments passed to other functions (not used at the moment).

See Also

AlphaPart for partitioning breeding values, plot.summaryAlphaPart for plotting output of summary method

Examples

## --- Partition additive genetic values by loc ---
res <- AlphaPart(x=AlphaPart.ped, colPath="country", colBV=c("bv1", "bv2"))

## Summarize whole population
ret <- summary(res)

## Summarize population by generation (=trend)
ret <- summary(res, by="gen")

## Summarize population by generation (=trend) but only for domestic location
ret <- summary(res, by="gen", subset=res[[1]]$country == "domestic")

## --- Partition additive genetic values by loc and gender ---

AlphaPart.ped$country.gender <- with(AlphaPart.ped, paste(country, gender, sep="-"))
res <- AlphaPart(x=AlphaPart.ped, colPath="country.gender", colBV=c("bv1", "bv2"))

## Summarize population by generation (=trend)
ret <- summary(res, by="gen")

## Summarize population by generation (=trend) but only for domestic location
ret <- summary(res, by="gen", subset=res[[1]]$country == "domestic")