R: A function to summarize AlphaPart object.

summary.AlphaPart {AlphaPart}

R Documentation

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.

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")