Cholesky-methods() R function from [Matrix]

Methods for Cholesky Factorization

Computes the pivoted Cholesky factorization of an $n-by-n$ real, symmetric matrix $A$ , which has the general form [REMOVE_ME] $P_1 A P_1' = L_1 D L_1' \overset{D_{jj} \ge 0}{=} L L'P1 * A * P1' = L1 * D * L1' [ = L * L' ] [REMOVE_ME_2]$

or (equivalently) [REMOVE_ME] $A = P_1' L_1 D L_1' P_1 \overset{D_{jj} \ge 0}{=} P_1' L L' P_1A = P1' L1 * D * L1' * P1 [ = P1' * L * L' * P1 ] [REMOVE_ME_2]$

where $P1$ is a permutation matrix, $L1$ is a unit lower triangular matrix, $D$ is a diagonal matrix, and $L = L1 * sqrt(D)$ . The second equalities hold only for positive semidefinite $A$ , for which the diagonal entries of $D$ are non-negative and $sqrt(D)$ is well-defined.

Methods for denseMatrix are built on LAPACK routines dpstrf, dpotrf, and dpptrf. The latter two do not permute rows or columns, so that $P1$ is an identity matrix.

Methods for sparseMatrix are built on CHOLMOD routines cholmod_analyze and cholmod_factorize_p.

methods

Description

Computes the pivoted Cholesky factorization of an $n-by-n$ real, symmetric matrix $A$ , which has the general form

P_1 A P_1' = L_1 D L_1' \overset{D_{jj} \ge 0}{=} L L'P1 * A * P1' = L1 * D * L1' [ = L * L' ]

or (equivalently)

A = P_1' L_1 D L_1' P_1 \overset{D_{jj} \ge 0}{=} P_1' L L' P_1A = P1' L1 * D * L1' * P1 [ = P1' * L * L' * P1 ]

Methods for denseMatrix are built on LAPACK routines dpstrf, dpotrf, and dpptrf. The latter two do not permute rows or columns, so that $P1$ is an identity matrix.

Methods for sparseMatrix are built on CHOLMOD routines cholmod_analyze and cholmod_factorize_p.


Cholesky(A, ...)
## S4 method for signature 'dsyMatrix'
Cholesky(A, perm = TRUE, tol = -1, ...)
## S4 method for signature 'dspMatrix'
Cholesky(A, ...)
## S4 method for signature 'dsCMatrix'
Cholesky(A, perm = TRUE, LDL = !super, super = FALSE,
    Imult = 0, ...)
## S4 method for signature 'ddiMatrix'
Cholesky(A, ...)
## S4 method for signature 'generalMatrix'
Cholesky(A, uplo = "U", ...)
## S4 method for signature 'triangularMatrix'
Cholesky(A, uplo = "U", ...)
## S4 method for signature 'matrix'
Cholesky(A, uplo = "U", ...)

Arguments

A: a finite , symmetric matrix or Matrix to be factorized. If A

is square but not symmetric, then it will be treated

as symmetric; see uplo. Methods for dense A require positive definiteness when perm = FALSE and positive semidefiniteness when perm = TRUE. Methods for sparse A require positive definiteness when LDL = TRUE and nonzero leading principal minors (after pivoting) when LDL = FALSE. Methods for sparse, diagonal A are an exception, requiring positive semidefiniteness unconditionally.
perm: a logical indicating if the rows and columns of $A$ should be pivoted. Methods for sparse A

employ the approximate minimum degree (AMD) algorithm in order to reduce fill-in, i.e., without regard for numerical stability. Pivoting for sparsity may introduce nonpositive leading principal minors, causing the factorization to fail, in which case it may be necessary to set perm = FALSE.
tol: a finite numeric tolerance, used only if perm = TRUE. The factorization algorithm stops if the pivot is less than or equal to tol. Negative tol is equivalent to nrow(A) * .Machine$double.eps * max(diag(A)).
LDL: a logical indicating if the simplicial factorization should be computed as $P1' * L1 * D * L1' * P1$ , such that the result stores the lower triangular entries of $L1-I+D$ . The alternative is $P1' * L * L' * P1$ , such that the result stores the lower triangular entries of $L = L1 * sqrt(D)$ . This argument is ignored if super = TRUE (or if super = NA

and the supernodal algorithm is chosen), as the supernodal code does not yet support the LDL = TRUE variant.
super: a logical indicating if the factorization should use the supernodal algorithm. The alternative is the simplicial algorithm. Setting super = NA leaves the choice to a CHOLMOD-internal heuristic.
Imult: a finite number. The matrix that is factorized is A + Imult * diag(nrow(A)), i.e., A plus Imult times the identity matrix. This argument is useful for symmetric, indefinite A, as Imult > max(rowSums(abs(A)) - diag(abs(A))) ensures that A + Imult * diag(nrow(A)) is diagonally dominant. (Symmetric, diagonally dominant matrices are positive definite.)
uplo: a string, either "U" or "L", indicating which triangle of A should be used to compute the factorization. The default is "U", even for lower triangular A, to be consistent with chol from base.
...: further arguments passed to or from methods.

Returns

An object representing the factorization, inheriting from virtual class CholeskyFactorization. For a traditional matrix A, the specific class is Cholesky. For A inheriting from unpackedMatrix, packedMatrix, and sparseMatrix, the specific class is Cholesky, pCholesky, and dCHMsimpl or dCHMsuper, respectively.

Details

Note that the result of a call to Cholesky inherits from CholeskyFactorization but not Matrix. Users who just want a matrix should consider using chol, whose methods are simple wrappers around Cholesky returning just the upper triangular Cholesky factor $L'$ , typically as a triangularMatrix. However, a more principled approach would be to construct factors as needed from the CholeskyFactorization object, e.g., with expand1(x, "L"), if x is the object.

The behaviour of Cholesky(A, perm = TRUE) for dense A

is somewhat exceptional, in that it expects without checking that A is positive semidefinite. By construction, if $A$

is positive semidefinite and the exact algorithm encounters a zero pivot, then the unfactorized trailing submatrix is the zero matrix, and there is nothing left to do. Hence when the finite precision algorithm encounters a pivot less than tol, it signals a warning instead of an error and zeros the trailing submatrix in order to guarantee that $P' * L * L' * P$ is positive semidefinite even if $A$ is not. It follows that one way to test for positive semidefiniteness of $A$ in the event of a warning is to analyze the error

\frac{\lVert A - P' L L' P \rVert}{\lVert A \rVert}\,.norm(A - P' * L * L' * P) / norm(A).

See the examples and LAPACK Working Note (LAWN ) 161 for details.

References

The LAPACK source code, including documentation; see https://netlib.org/lapack/double/dpstrf.f, https://netlib.org/lapack/double/dpotrf.f, and https://netlib.org/lapack/double/dpptrf.f.

The CHOLMOD source code; see https://github.com/DrTimothyAldenDavis/SuiteSparse, notably the header file CHOLMOD/Include/cholmod.h

defining cholmod_factor_struct.

Lucas, C. (2004). LAPACK-style codes for level 2 and 3 pivoted Cholesky factorizations. LAPACK Working Note, Number 161. https://www.netlib.org/lapack/lawnspdf/lawn161.pdf

Chen, Y., Davis, T. A., Hager, W. W., & Rajamanickam, S. (2008). Algorithm 887: CHOLMOD, supernodal sparse Cholesky factorization and update/downdate. ACM Transactions on Mathematical Software, 35(3), Article 22, 1-14. tools:::Rd_expr_doi("10.1145/1391989.1391995")

Amestoy, P. R., Davis, T. A., & Duff, I. S. (2004). Algorithm 837: AMD, an approximate minimum degree ordering algorithm. ACM Transactions on Mathematical Software, 17(4), 886-905. tools:::Rd_expr_doi("10.1145/1024074.1024081")

Golub, G. H., & Van Loan, C. F. (2013). Matrix computations (4th ed.). Johns Hopkins University Press. tools:::Rd_expr_doi("10.56021/9781421407944")

Examples


showMethods("Cholesky", inherited = FALSE)
set.seed(0)

## ---- Dense ----------------------------------------------------------

## .... Positive definite ..............................................

n <- 6L
(A1 <- crossprod(Matrix(rnorm(n * n), n, n)))
(ch.A1.nopivot <- Cholesky(A1, perm = FALSE))
(ch.A1 <- Cholesky(A1))
stopifnot(exprs = {
    length(ch.A1@perm) == ncol(A1)
    isPerm(ch.A1@perm)
    is.unsorted(ch.A1@perm) # typically not the identity permutation
    length(ch.A1.nopivot@perm) == 0L
})

## A ~ P1' L D L' P1 ~ P1' L L' P1 in floating point
str(e.ch.A1 <- expand2(ch.A1, LDL =  TRUE), max.level = 2L)
str(E.ch.A1 <- expand2(ch.A1, LDL = FALSE), max.level = 2L)
stopifnot(exprs = {
    all.equal(as(A1, "matrix"), as(Reduce(`%*%`, e.ch.A1), "matrix"))
    all.equal(as(A1, "matrix"), as(Reduce(`%*%`, E.ch.A1), "matrix"))
})

## .... Positive semidefinite but not positive definite ................

A2 <- A1
A2[1L, ] <- A2[, 1L] <- 0
A2
try(Cholesky(A2, perm = FALSE)) # fails as not positive definite
ch.A2 <- Cholesky(A2) # returns, with a warning and ...
A2.hat <- Reduce(`%*%`, expand2(ch.A2, LDL = FALSE))
norm(A2 - A2.hat, "2") / norm(A2, "2") # 7.670858e-17

## .... Not positive semidefinite ......................................

A3 <- A1
A3[1L, ] <- A3[, 1L] <- -1
A3
try(Cholesky(A3, perm = FALSE)) # fails as not positive definite
ch.A3 <- Cholesky(A3) # returns, with a warning and ...
A3.hat <- Reduce(`%*%`, expand2(ch.A3, LDL = FALSE))
norm(A3 - A3.hat, "2") / norm(A3, "2") # 1.781568

## Indeed, 'A3' is not positive semidefinite, but 'A3.hat' _is_
ch.A3.hat <- Cholesky(A3.hat)
A3.hat.hat <- Reduce(`%*%`, expand2(ch.A3.hat, LDL = FALSE))
norm(A3.hat - A3.hat.hat, "2") / norm(A3.hat, "2") # 1.777944e-16

## ---- Sparse ---------------------------------------------------------

## Really just three cases modulo permutation :
##
##            type        factorization  minors of P1 A P1'
##   1  simplicial  P1 A P1' = L1 D L1'             nonzero
##   2  simplicial  P1 A P1' = L    L '            positive
##   3  supernodal  P1 A P2' = L    L '            positive

data(KNex, package = "Matrix")
A4 <- crossprod(KNex[["mm"]])

ch.A4 <-
list(pivoted =
     list(simpl1 = Cholesky(A4, perm =  TRUE, super = FALSE, LDL =  TRUE),
          simpl0 = Cholesky(A4, perm =  TRUE, super = FALSE, LDL = FALSE),
          super0 = Cholesky(A4, perm =  TRUE, super =  TRUE             )),
     unpivoted =
     list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, LDL =  TRUE),
          simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, LDL = FALSE),
          super0 = Cholesky(A4, perm = FALSE, super =  TRUE             )))
ch.A4

s <- simplify2array
rapply2 <- function(object, f, ...) rapply(object, f, , , how = "list", ...)

s(rapply2(ch.A4, isLDL))
s(m.ch.A4 <- rapply2(ch.A4, expand1, "L")) # giving L = L1 sqrt(D)

## By design, the pivoted and simplicial factorizations
## are more sparse than the unpivoted and supernodal ones ...
s(rapply2(m.ch.A4, object.size))

## Which is nicely visualized by lattice-based methods for 'image'
inm <- c("pivoted", "unpivoted")
jnm <- c("simpl1", "simpl0", "super0")
for(i in 1:2)
  for(j in 1:3)
    print(image(m.ch.A4[[c(i, j)]], main = paste(inm[i], jnm[j])),
          split = c(j, i, 3L, 2L), more = i * j < 6L)

simpl1 <- ch.A4[[c("pivoted", "simpl1")]]
stopifnot(exprs = {
    length(simpl1@perm) == ncol(A4)
    isPerm(simpl1@perm, 0L)
    is.unsorted(simpl1@perm) # typically not the identity permutation
})

## One can expand with and without D regardless of isLDL(.),
## but "without" requires L = L1 sqrt(D), which is conditional
## on min(diag(D)) >= 0, hence "with" is the default
isLDL(simpl1)
stopifnot(min(diag(simpl1)) >= 0)
str(e.ch.A4 <- expand2(simpl1, LDL =  TRUE), max.level = 2L) # default
str(E.ch.A4 <- expand2(simpl1, LDL = FALSE), max.level = 2L)
stopifnot(exprs = {
    all.equal(E.ch.A4[["L" ]], e.ch.A4[["L1" ]] %*% sqrt(e.ch.A4[["D"]]))
    all.equal(E.ch.A4[["L."]], sqrt(e.ch.A4[["D"]]) %*% e.ch.A4[["L1."]])
    all.equal(A4, as(Reduce(`%*%`, e.ch.A4), "symmetricMatrix"))
    all.equal(A4, as(Reduce(`%*%`, E.ch.A4), "symmetricMatrix"))
})

## The "same" permutation matrix with "alternate" representation
## [i, perm[i]] {margin=1} <-> [invertPerm(perm)[j], j] {margin=2}
alt <- function(P) {
    P@margin <- 1L + !(P@margin - 1L) # 1 <-> 2
    P@perm <- invertPerm(P@perm)
    P
}

## Expansions are elegant but inefficient (transposes are redundant)
## hence programmers should consider methods for 'expand1' and 'diag'
stopifnot(exprs = {
    identical(expand1(simpl1, "P1"), alt(e.ch.A4[["P1"]]))
    identical(expand1(simpl1, "L"), E.ch.A4[["L"]])
    identical(Diagonal(x = diag(simpl1)), e.ch.A4[["D"]])
})

## chol(A, pivot = value) is a simple wrapper around
## Cholesky(A, perm = value, LDL = FALSE, super = FALSE),
## returning L' = sqrt(D) L1' _but_ giving no information
## about the permutation P1
selectMethod("chol", "dsCMatrix")
stopifnot(all.equal(chol(A4, pivot = TRUE), E.ch.A4[["L."]]))

## Now a symmetric matrix with positive _and_ negative eigenvalues,
## hence _not_ positive semidefinite
A5 <- new("dsCMatrix",
          Dim = c(7L, 7L),
          p = c(0:1, 3L, 6:7, 10:11, 15L),
          i = c(0L, 0:1, 0:3, 2:5, 3:6),
          x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, -16, -128, -2, -67))
(ev <- eigen(A5, only.values = TRUE)$values)
(t.ev <- table(factor(sign(ev), -1:1))) # the matrix "inertia"

ch.A5 <- Cholesky(A5)
isLDL(ch.A5)
(d.A5 <- diag(ch.A5)) # diag(D) is partly negative

## Sylvester's law of inertia holds here, but not in general
## in finite precision arithmetic
stopifnot(identical(table(factor(sign(d.A5), -1:1)), t.ev))

try(expand1(ch.A5, "L"))         # unable to compute L = L1 sqrt(D)
try(expand2(ch.A5, LDL = FALSE)) # ditto
try(chol(A5, pivot = TRUE))      # ditto

## The default expansion is "square root free" and still works here
str(e.ch.A5 <- expand2(ch.A5, LDL = TRUE), max.level = 2L)
stopifnot(all.equal(A5, as(Reduce(`%*%`, e.ch.A5), "symmetricMatrix")))

## Version of the SuiteSparse library, which includes CHOLMOD
Mv <- Matrix.Version()
Mv[["suitesparse"]]

Matrix package Read PDF manual

Maintainer: Martin Maechler
License: GPL (>= 2) | file LICENCE
Last published: 2025-03-11

Useful links

Cholesky-methods function