Compute a common shared environment matrix

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.

extended.shared(id, rho = 1, theta = 1, ...)

# S3 method for class 'pedigreeList'
extended.shared(id, rho = 1, theta = 1, ...)

# S3 method for class 'pedigree'
extended.shared(id, rho = 1, theta = 1, ...)

Arguments

id

either a pedigree object or pedigreeList object

rho

The correlation between spouses

theta

The partial path coefficient from parents to offspring

...

Any number of optional arguments. Not used at the moment

Value

a matrix of shared environment coefficients

Details

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.

See also

pedigree, kinship,

Author

Claus Ekstrom claus@rprimer.dk

Examples

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, 0, 2, 2, 4, 0,  6,  8,  0, 10, 11),
                    dad =c(0, 0, 0, 0, 0, 1, 1, 3, 0,  5,  7,  0,  9, 12),
                    sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1,  2,  2,  1,  2,  2))

tped <- with(test1, pedigree(id, dad, mom, sex))
extended.shared(tped)
#>       1    2    3    4    5    6    7    8   9    10    11  12     13     14
#> 1  1.00 1.00 0.00 0.00 0.00 1.00 1.00 0.00 0.0 0.500 0.500 0.0 0.2500 0.2500
#> 2  1.00 1.00 0.00 0.00 0.00 1.00 1.00 0.00 0.0 0.500 0.500 0.0 0.2500 0.2500
#> 3  0.00 0.00 1.00 1.00 0.00 0.00 0.00 1.00 0.0 0.000 0.500 0.0 0.0000 0.2500
#> 4  0.00 0.00 1.00 1.00 0.00 0.00 0.00 1.00 0.0 0.000 0.500 0.0 0.0000 0.2500
#> 5  0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.0 0.500 0.000 0.0 0.2500 0.0000
#> 6  1.00 1.00 0.00 0.00 0.00 1.00 1.00 0.00 0.0 0.500 0.500 0.0 0.2500 0.2500
#> 7  1.00 1.00 0.00 0.00 0.00 1.00 1.00 0.00 0.0 0.500 0.500 0.0 0.2500 0.2500
#> 8  0.00 0.00 1.00 1.00 0.00 0.00 0.00 1.00 0.0 0.000 0.500 0.0 0.0000 0.2500
#> 9  0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.0 0.000 0.000 0.0 0.5000 0.0000
#> 10 0.50 0.50 0.00 0.00 0.50 0.50 0.50 0.00 0.0 0.500 0.250 0.0 0.2500 0.1250
#> 11 0.50 0.50 0.50 0.50 0.00 0.50 0.50 0.50 0.0 0.250 0.500 0.0 0.1250 0.2500
#> 12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.0 0.000 0.000 1.0 0.0000 0.5000
#> 13 0.25 0.25 0.00 0.00 0.25 0.25 0.25 0.00 0.5 0.250 0.125 0.0 0.3750 0.0625
#> 14 0.25 0.25 0.25 0.25 0.00 0.25 0.25 0.25 0.0 0.125 0.250 0.5 0.0625 0.3750