mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees


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Documentation for package ‘kinship’ version 1.1.0-23

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%*% Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%-method Class "bdsmatrix"
%*%-method Class "gchol.bdsmatrix"
%*%-method Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%-methods Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%.default Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%.gchol.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
align.pedigree Generate plotting information for a pedigree
alignped1 Generate plotting information for a pedigree
alignped2 Generate plotting information for a pedigree
alignped3 Generate plotting information for a pedigree
alignped4 Generate plotting information for a pedigree
all-method Class "bdsmatrix"
any-method Class "bdsmatrix"
as.matrix.bdsmatrix a function for bdsmatrix
as.matrix.gchol Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
as.matrix.gchol.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
as.vector.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
autohint Align a pedigree to print well
bdsBlock Block diagonal matrices.
bdsI Sparse identity matrices
bdsmatrix Create a sparse symmetric block diagonal matrix object
bdsmatrix-class Class "bdsmatrix"
bdsmatrix.ibd Create a bdsmatrix from a list
bdsmatrix.reconcile Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
besthint Create a hints matrix for a pedigree.
coerce-method Class "bdsmatrix"
coerce-method Class "gchol"
coerce-method Class "gchol.bdsmatrix"
coxme Fit a mixed-effects Cox model
coxme.control Control parameters for coxme
coxme.fit Fit a mixed-effects Cox model
coxme.varcheck Fit a mixed-effects Cox model
diag-method Class "bdsmatrix"
diag-method Class "gchol"
diag-method Class "gchol.bdsmatrix"
diag<--method Class "bdsmatrix"
dim-method Class "bdsmatrix"
dim-method Class "gchol.bdsmatrix"
dimnames-method Class "bdsmatrix"
dimnames<--method Class "bdsmatrix"
familycheck Error check for a family classification
gchol Generalized Cholesky decompostion
gchol-class Class "gchol"
gchol-method Methods for Function gchol in Package 'kinship'
gchol-methods Methods for Function gchol in Package 'kinship'
gchol.bdsmatrix Generalized Cholesky decompostion
gchol.bdsmatrix-class Class "gchol.bdsmatrix"
getCovariateFormula2 Linear Mixed Effects model using a kinship matrix.
getCrossedTerms Linear Mixed Effects model using a kinship matrix.
getGroupsFormula2 Linear Mixed Effects model using a kinship matrix.
is.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.gchol.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.list.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.list.gchol.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.matrix.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.matrix.gchol.bdsmatrix Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
kindepth Compute a kinship matrix
kinship Compute a kinship matrix
list or NULL-class Class "list or NULL"
lmekin Linear Mixed Effects model using a kinship matrix.
makefamid Identify family groups
makekinship Create a sparse kinship matrix
Math-method Class "bdsmatrix"
Math2-method Class "bdsmatrix"
max-method Class "bdsmatrix"
min-method Class "bdsmatrix"
Ops-method Class "bdsmatrix"
pedigree Create pedigree structure
plot.pedigree plot pedigrees
print.bdsmatrix Create a sparse symmetric block diagonal matrix object
print.coxme Fit a mixed-effects Cox model
print.lmekin Linear Mixed Effects model using a kinship matrix.
prod-method Class "bdsmatrix"
range-method Class "bdsmatrix"
show-method Class "bdsmatrix"
show-method Class "gchol"
show-method Class "gchol.bdsmatrix"
solve.bdsmatrix Solve a matrix equation using the generalized Cholesky decompostion
solve.gchol Solve a matrix equation using the generalized Cholesky decompostion
solve.gchol.bdsmatrix function solve for gchol.bdsmatrix
strata2 Control parameters for coxme
sum-method Class "bdsmatrix"
unique-method Class "bdsmatrix"
[-method Class "bdsmatrix"
[-method Class "gchol.bdsmatrix"
[.pedigree Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix