summary.AlphaPart: A function to summarize AlphaPart object.

In AlphaPart: Partition/Decomposition of Breeding Values by Paths of Information

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 class 'AlphaPart'
summary(object, by, FUN, labelSum, subset,
  sums, cov,  ...)

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).

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.

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")

AlphaPart documentation built on Nov. 16, 2022, 1:09 a.m.