AlphaPartSubset.R
AlphaPartSubset.RdA function to choose the partition paths to keep.
Arguments
- x
AlphaPart or summaryAlphaPart, object from the
AlphaPart(...)orsummary(AlphaPart(...), ...)call.- paths
Character, names of paths to be kept.
Value
An object of class AlphaPart or summaryAlphaPart with only some paths.
Meta information in slot "info" is modified as well.
Details
Displaying results of partitions for many paths is often confusing.
This function helps in selecting only paths of interest.
Unspecified paths are removed from the input object x.
Meta information is modified accordingly. Default setting does nothing.
See also
AlphaPart for the main method,
summary.AlphaPart for summary method that works on output of AlphaPart,
AlphaPartSum for sum 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, 100, 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 1 100 103.3333 -3.333333 100.0 0.0
#> 2 2 0 0 B 1 110 103.3333 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 2 100 103.3333 -3.333333 0.0 100.0
#> 5 5 4 3 A 3 85 102.5000 -17.500000 7.5 77.5
#> 6 6 0 3 A 3 110 52.5000 57.500000 82.5 27.5
#>
## Keep some partitions (working on object of class AlphaPart)
(tmp2 <- AlphaPartSubset(x=tmp, paths="A"))
#>
#>
#> Partitions of breeding values
#> - individuals: 6
#> - paths: 1 (A)
#> - traits: 2 (trt1, trt2)
#> - warning: Consistency of the overall sum of partitions might not be correct due to the previous use of 'AlphaPartPathSubset'
#>
#> Trait: trt1
#>
#> id fid mid loc gen trt1 trt1_pa trt1_w trt1_A
#> 1 1 0 0 A 1 100 116.6667 -16.666667 100
#> 2 2 0 0 B 1 120 116.6667 3.333333 0
#> 3 3 2 1 A 2 115 110.0000 5.000000 55
#> 4 4 0 0 B 2 130 116.6667 13.333333 0
#> 5 5 4 3 A 3 125 122.5000 2.500000 30
#> 6 6 0 3 A 3 125 57.5000 67.500000 95
#>
#> Trait: trt2
#>
#> id fid mid loc gen trt2 trt2_pa trt2_w trt2_A
#> 1 1 0 0 A 1 100 103.3333 -3.333333 100.0
#> 2 2 0 0 B 1 110 103.3333 6.666667 0.0
#> 3 3 2 1 A 2 105 105.0000 0.000000 50.0
#> 4 4 0 0 B 2 100 103.3333 -3.333333 0.0
#> 5 5 4 3 A 3 85 102.5000 -17.500000 7.5
#> 6 6 0 3 A 3 110 52.5000 57.500000 82.5
#>
## 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 2 102.5 25 77.5
#> 3 3 2 97.5 45 52.5
#>
## Keep some partitions (working on object of class summaryAlphaPart)
(tmpS2 <- AlphaPartSubset(x=tmpS, paths="A"))
#>
#>
#> Summary of partitions of breeding values
#> - paths: 1 (A)
#> - traits: 2 (trt1, trt2)
#> - warning: Consistency of the overall sum of partitions might not be correct due to the previous use of 'AlphaPartPathSubset'
#>
#> Trait: trt1
#>
#> gen N Sum A
#> 1 1 2 110.0 50.0
#> 2 2 2 122.5 27.5
#> 3 3 2 125.0 62.5
#>
#> Trait: trt2
#>
#> gen N Sum A
#> 1 1 2 105.0 50
#> 2 2 2 102.5 25
#> 3 3 2 97.5 45
#>
## ... must be equal to
(tmpS3 <- summary(tmp2, by="gen"))
#>
#>
#> Summary of partitions of breeding values
#> - paths: 1 (A)
#> - traits: 2 (trt1, trt2)
#> - warning: Consistency of the overall sum of partitions might not be correct due to the previous use of 'AlphaPartPathSubset'
#>
#> Trait: trt1
#>
#> gen N Sum A
#> 1 1 2 110.0 50.0
#> 2 2 2 122.5 27.5
#> 3 3 2 125.0 62.5
#>
#> Trait: trt2
#>
#> gen N Sum A
#> 1 1 2 105.0 50
#> 2 2 2 102.5 25
#> 3 3 2 97.5 45
#>