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

AlphaPartSum

R Documentation

AlphaPartSum.R

Description

A function to sum partitions of several paths.

Usage

AlphaPartSum(
  x,
  map = NULL,
  remove = TRUE,
  zeroPath = TRUE,
  call = "AlphaPartSum"
)

Arguments

`x`	summaryAlphaPart, object from the `AlphaPart(...)` or `summary(AlphaPart(...), ...)` call.
`map`	List, a map of summing paths; see details and examples.
`remove`	Logical, remove original paths or not.
`zeroPath`	Logical, set called path to zero if it does not exist.
`call`	character, for internal use with `AlphaPartSubset`).

Details

Sometimes partitions of particular paths are very small or we want to sum paths that have some similarity. These actions are easy to achive manually but this functions provides a way to do this consistently with the given object x.

Arguments map must be a list of vectors of length at least two. Vectors of length one are skipped. The idea is that the first element is the new or existing path into which we add up all the remaining specified paths, say list(c("A", "B"), c("X", "X", "Y"), c("Z", "X")) would imply A = B, X = X + Y, and Z = X = X + Y. Note that once X is changed its changed value is used in further calculations. Specify different (new) names for new targets if you want to avoid this.

Be carefull with remove=TRUE, which is the default setting, as all partitions defined after the first (target/new) partition in vector in list will be removed, for example with list(c("A", "B"), c("X", "X", "Y"), c("Z", "X")) partitions B and Y will be removed, while X will not be removed as it is defined as a target/new partition.

Value

An object of class AlphaPart or summaryAlphaPart with modified partitions. Meta information in slot "info" is modified as well.

Examples

## Small pedigree with additive genetic (=breeding) values
ped <- data.frame(  id=c(  1,   2,   3,   4,   5,   6),
                  fid=c(  0,   0,   2,   0,   4,   0),
                  mid=c(  0,   0,   1,   0,   3,   3),
                  loc=c("A", "B", "A", "B", "A", "A"),
                  gen=c(  1,   1,   2,   2,   3,   3),
                 trt1=c(100, 120, 115, 130, 125, 125),
                 trt2=c(100, 110, 105,  140,  85, 110))

## Partition additive genetic values
(tmp <- AlphaPart(x=ped, colBV=c("trt1", "trt2")))

## Sum some partitions (working on object of class AlphaPart)
(tmp2 <- AlphaPartSum(x=tmp, map=list(c("X", "A", "B"), c("A", "B"))))

## Summarize by generation
(tmpS <- summary(tmp, by="gen"))

## Sum some partitions (working on object of class summaryAlphaPart)
(tmpS2 <- AlphaPartSum(x=tmpS, map=list(c("X", "A", "B"), c("A", "B"))))

## ... must be equal to
(tmpS3 <- summary(tmp2, by="gen"))

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