AlphaPartSum.R
AlphaPartSum.RdA function to sum partitions of several paths.
Arguments
- x
summaryAlphaPart, object from the
AlphaPart(...)orsummary(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).
Value
An object of class AlphaPart or summaryAlphaPart with modified partitions.
Meta information in slot "info" is modified as well.
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.
See also
AlphaPart for the main method,
summary.AlphaPart for summary method that works on output of AlphaPart,
AlphaPartSubset for subset/keep method
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")))
#>
#> Size:
#> - individuals: 6
#> - traits: 2 (trt1, trt2)
#> - paths: 2 (A, B)
#> - unknown (missing) values:
#> trt1 trt2
#> 0 0
#>
#>
#> Partitions of breeding values
#> - individuals: 6
#> - paths: 2 (A, B)
#> - traits: 2 (trt1, trt2)
#>
#> Trait: trt1
#>
#> id fid mid loc gen trt1 trt1_pa trt1_w trt1_A trt1_B
#> 1 1 0 0 A 1 100 116.6667 -16.666667 100 0
#> 2 2 0 0 B 1 120 116.6667 3.333333 0 120
#> 3 3 2 1 A 2 115 110.0000 5.000000 55 60
#> 4 4 0 0 B 2 130 116.6667 13.333333 0 130
#> 5 5 4 3 A 3 125 122.5000 2.500000 30 95
#> 6 6 0 3 A 3 125 57.5000 67.500000 95 30
#>
#> Trait: trt2
#>
#> id fid mid loc gen trt2 trt2_pa trt2_w trt2_A trt2_B
#> 1 1 0 0 A 1 100 116.6667 -16.666667 100.0 0.0
#> 2 2 0 0 B 1 110 116.6667 -6.666667 0.0 110.0
#> 3 3 2 1 A 2 105 105.0000 0.000000 50.0 55.0
#> 4 4 0 0 B 2 140 116.6667 23.333333 0.0 140.0
#> 5 5 4 3 A 3 85 122.5000 -37.500000 -12.5 97.5
#> 6 6 0 3 A 3 110 52.5000 57.500000 82.5 27.5
#>
## Sum some partitions (working on object of class AlphaPart)
(tmp2 <- AlphaPartSum(x=tmp, map=list(c("X", "A", "B"), c("A", "B"))))
#>
#>
#> Partitions of breeding values
#> - individuals: 6
#> - paths: 2 (A, X)
#> - traits: 2 (trt1, trt2)
#> - warning: Consistency of the overall sum of partitions might not be correct due to the previous use of 'AlphaPartSum'
#>
#> Trait: trt1
#>
#> id fid mid loc gen trt1 trt1_pa trt1_w trt1_A trt1_X
#> 1 1 0 0 A 1 100 116.6667 -16.666667 0 100
#> 2 2 0 0 B 1 120 116.6667 3.333333 120 120
#> 3 3 2 1 A 2 115 110.0000 5.000000 60 115
#> 4 4 0 0 B 2 130 116.6667 13.333333 130 130
#> 5 5 4 3 A 3 125 122.5000 2.500000 95 125
#> 6 6 0 3 A 3 125 57.5000 67.500000 30 125
#>
#> Trait: trt2
#>
#> id fid mid loc gen trt2 trt2_pa trt2_w trt2_A trt2_X
#> 1 1 0 0 A 1 100 116.6667 -16.666667 0.0 100
#> 2 2 0 0 B 1 110 116.6667 -6.666667 110.0 110
#> 3 3 2 1 A 2 105 105.0000 0.000000 55.0 105
#> 4 4 0 0 B 2 140 116.6667 23.333333 140.0 140
#> 5 5 4 3 A 3 85 122.5000 -37.500000 97.5 85
#> 6 6 0 3 A 3 110 52.5000 57.500000 27.5 110
#>
## Summarize by generation
(tmpS <- summary(tmp, by="gen"))
#>
#>
#> Summary of partitions of breeding values
#> - paths: 2 (A, B)
#> - traits: 2 (trt1, trt2)
#>
#> Trait: trt1
#>
#> gen N Sum A B
#> 1 1 2 110.0 50.0 60.0
#> 2 2 2 122.5 27.5 95.0
#> 3 3 2 125.0 62.5 62.5
#>
#> Trait: trt2
#>
#> gen N Sum A B
#> 1 1 2 105.0 50 55.0
#> 2 2 2 122.5 25 97.5
#> 3 3 2 97.5 35 62.5
#>
## Sum some partitions (working on object of class summaryAlphaPart)
(tmpS2 <- AlphaPartSum(x=tmpS, map=list(c("X", "A", "B"), c("A", "B"))))
#>
#>
#> Summary of partitions of breeding values
#> - paths: 2 (A, X)
#> - traits: 2 (trt1, trt2)
#> - warning: Consistency of the overall sum of partitions might not be correct due to the previous use of 'AlphaPartSum'
#>
#> Trait: trt1
#>
#> gen N Sum A X
#> 1 1 2 110.0 60.0 110.0
#> 2 2 2 122.5 95.0 122.5
#> 3 3 2 125.0 62.5 125.0
#>
#> Trait: trt2
#>
#> gen N Sum A X
#> 1 1 2 105.0 55.0 105.0
#> 2 2 2 122.5 97.5 122.5
#> 3 3 2 97.5 62.5 97.5
#>
## ... must be equal to
(tmpS3 <- summary(tmp2, by="gen"))
#>
#>
#> Summary of partitions of breeding values
#> - paths: 2 (A, X)
#> - traits: 2 (trt1, trt2)
#> - warning: Consistency of the overall sum of partitions might not be correct due to the previous use of 'AlphaPartSum'
#>
#> Trait: trt1
#>
#> gen N Sum A X
#> 1 1 2 110.0 60.0 110.0
#> 2 2 2 122.5 95.0 122.5
#> 3 3 2 125.0 62.5 125.0
#>
#> Trait: trt2
#>
#> gen N Sum A X
#> 1 1 2 105.0 55.0 105.0
#> 2 2 2 122.5 97.5 122.5
#> 3 3 2 97.5 62.5 97.5
#>