chol {base}R Documentation

The Choleski Decomposition


Compute the Choleski factorization of a real symmetric positive-definite square matrix.


chol(x, ...)

## Default S3 method:
chol(x, pivot = FALSE,  LINPACK = FALSE, tol = -1, ...)



an object for which a method exists. The default method applies to numeric (or logical) symmetric, positive-definite matrices.


arguments to be based to or from methods.


Should pivoting be used?


logical. Should LINPACK be used (now ignored)?


A numeric tolerance for use with pivot = TRUE.


chol is generic: the description here applies to the default method.

Note that only the upper triangular part of x is used, so that R'R = x when x is symmetric.

If pivot = FALSE and x is not non-negative definite an error occurs. If x is positive semi-definite (i.e., some zero eigenvalues) an error will also occur as a numerical tolerance is used.

If pivot = TRUE, then the Choleski decomposition of a positive semi-definite x can be computed. The rank of x is returned as attr(Q, "rank"), subject to numerical errors. The pivot is returned as attr(Q, "pivot"). It is no longer the case that t(Q) %*% Q equals x. However, setting pivot <- attr(Q, "pivot") and oo <- order(pivot), it is true that t(Q[, oo]) %*% Q[, oo] equals x, or, alternatively, t(Q) %*% Q equals x[pivot, pivot]. See the examples.

The value of tol is passed to LAPACK, with negative values selecting the default tolerance of (usually) nrow(x) * .Machine$double.neg.eps * max(diag(x)). The algorithm terminates once the pivot is less than tol.

Unsuccessful results from the underlying LAPACK code will result in an error giving a positive error code: these can only be interpreted by detailed study of the FORTRAN code.


The upper triangular factor of the Choleski decomposition, i.e., the matrix R such that R'R = x (see example).

If pivoting is used, then two additional attributes "pivot" and "rank" are also returned.


The code does not check for symmetry.

If pivot = TRUE and x is not non-negative definite then there will be a warning message but a meaningless result will occur. So only use pivot = TRUE when x is non-negative definite by construction.


This is an interface to the LAPACK routines DPOTRF and DPSTRF,

LAPACK is from and its guide is listed in the references.


Anderson. E. and ten others (1999) LAPACK Users' Guide. Third Edition. SIAM.
Available on-line at

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

See Also

chol2inv for its inverse (without pivoting), backsolve for solving linear systems with upper triangular left sides.

qr, svd for related matrix factorizations.


( m <- matrix(c(5,1,1,3),2,2) )
( cm <- chol(m) )
t(cm) %*% cm  #-- = 'm'
crossprod(cm)  #-- = 'm'

# now for something positive semi-definite
x <- matrix(c(1:5, (1:5)^2), 5, 2)
x <- cbind(x, x[, 1] + 3*x[, 2])
colnames(x) <- letters[20:22]
m <- crossprod(x)
qr(m)$rank # is 2, as it should be

# chol() may fail, depending on numerical rounding:
# chol() unlike qr() does not use a tolerance.

(Q <- chol(m, pivot = TRUE))
## we can use this by
pivot <- attr(Q, "pivot")
crossprod(Q[, order(pivot)]) # recover m

## now for a non-positive-definite matrix
( m <- matrix(c(5,-5,-5,3), 2, 2) )
try(chol(m))  # fails
(Q <- chol(m, pivot = TRUE)) # warning
crossprod(Q)  # not equal to m

[Package base version 3.4.4 Index]