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A function to summarize AlphaPart object.

summary.AlphaPart.Rd

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,  ...)

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"))
#> 
#> Size:
#>  - individuals: 8 
#>  - traits: 2 (bv1, bv2)
#>  - paths: 2 (domestic, import)
#>  - unknown (missing) values:
#> bv1 bv2 
#>   0   0 

## 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"))
#> 
#> Size:
#>  - individuals: 8 
#>  - traits: 2 (bv1, bv2)
#>  - paths: 4 (domestic-F, domestic-M, import-F, import-M)
#>  - unknown (missing) values:
#> bv1 bv2 
#>   0   0 

## 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")