Compute the common shared environment matrix for a set of related subjects. The function is generic, and can accept a pedigree, or pedigreeList as the first argument.
common.shared(id, ...) # S3 method for pedigreeList common.shared(id, ...) # S3 method for pedigree common.shared(id, ...)
| id | either a pedigree object or pedigreeList object |
|---|---|
| … | Any number of optional arguments. Not used at the moment |
a matrix of shared environment coefficients
When called with a pedigreeList, i.e., with multiple families, the routine will create a block-diagonal-symmetric `bdsmatrix' object. Since the [i,j] value of the result is 0 for any two unrelated individuals i and j and a `bdsmatix' utilizes sparse representation, the resulting object is often orders of magnitude smaller than an ordinary matrix. When called with a single pedigree and ordinary matrix is returned.
pedigree, kinship,
library(kinship2) test1 <- data.frame(id =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14), mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6, 2, 0, 0, 12, 13), dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3, 7, 0, 0, 11, 10), sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 2, 2, 2)) tped <- with(test1, pedigree(id, dad, mom, sex)) common.shared(tped)#> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 #> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 8 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 9 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 10 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 11 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 12 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 13 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 14 1 1 1 1 1 1 1 1 1 1 1 1 1 1