# Cholesky: Methods for Cholesky Factorization In Matrix: Sparse and Dense Matrix Classes and Methods

 Cholesky-methods R Documentation

## Methods for Cholesky Factorization

### Description

Computes the pivoted Cholesky factorization of an n \times n real, symmetric matrix A, which has the general form \SdeqnP_1 A P_1' = L_1 D L_1' \\\\oversetD_jj \\\\ge 0= L L'P1 * A * P1' = L1 * D * L1' [ = L * L' ] or (equivalently) \SdeqnA = P_1' L_1 D L_1' P_1 \\\\oversetD_jj \\\\ge 0= P_1' L L' P_1A = P1' L1 * D * L1' * P1 [ = P1' * L * L' * P1 ] where P_1 is a permutation matrix, L_1 is a unit lower triangular matrix, D is a diagonal matrix, and L = L_1 \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 P_1 is an identity matrix.

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

### Usage

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", ...)


 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 P_1' L_1 D L_1' P_1, such that the result stores the lower triangular entries of L_1-I+D. The alternative is P_1' L L' P_1, such that the result stores the lower triangular entries of L = L_1 \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. ### 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 \Sdeqn\\\\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. ### Value 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. ### 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. \Sexpr[results=rd]{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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1145/1024074.1024081")} Golub, G. H., & Van Loan, C. F. (2013). Matrix computations (4th ed.). Johns Hopkins University Press. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.56021/9781421407944")} ### See Also Classes Cholesky, pCholesky, dCHMsimpl and dCHMsuper and their methods. Classes dpoMatrix, dppMatrix, and dsCMatrix. Generic function chol, for obtaining the upper triangular Cholesky factor L' as a matrix or Matrix. Generic functions expand1 and expand2, for constructing matrix factors from the result. Generic functions BunchKaufman, Schur, lu, and qr, for computing other factorizations. ### 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 documentation built on Nov. 14, 2023, 5:06 p.m.