nmNearPD: C++ implementation of Matrix's nearPD

In nlmixr2est: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

C++ implementation of Matrix's nearPD

Description

With 'ensureSymmetry' it makes sure it is symmetric by applying 0.5*(t(x) + x) before using nmNearPD

Usage

nmNearPD(
  x,
  keepDiag = FALSE,
  do2eigen = TRUE,
  doDykstra = TRUE,
  only.values = FALSE,
  ensureSymmetry = !isSymmetric(x),
  eig.tol = 1e-06,
  conv.tol = 1e-07,
  posd.tol = 1e-08,
  maxit = 100L,
  trace = FALSE
)

Arguments

x	numeric n \times n approximately positive definite matrix, typically an approximation to a correlation or covariance matrix. If x is not symmetric (and ensureSymmetry is not false), symmpart(x) is used.
keepDiag	logical, generalizing corr: if TRUE, the resulting matrix should have the same diagonal (diag(x)) as the input matrix.
do2eigen	logical indicating if a posdefify() eigen step should be applied to the result of the Higham algorithm.
doDykstra	logical indicating if Dykstra's correction should be used; true by default. If false, the algorithm is basically the direct fixpoint iteration Y_k = P_U(P_S(Y_{k-1})).
only.values	logical; if TRUE, the result is just the vector of eigenvalues of the approximating matrix.
ensureSymmetry	logical; by default, symmpart(x) is used whenever isSymmetric(x) is not true. The user can explicitly set this to TRUE or FALSE, saving the symmetry test. Beware however that setting it FALSE for an asymmetric input x, is typically nonsense!
eig.tol	defines relative positiveness of eigenvalues compared to largest one, \lambda_1. Eigenvalues \lambda_k are treated as if zero when \lambda_k / \lambda_1 \le eig.tol.
conv.tol	convergence tolerance for Higham algorithm.
posd.tol	tolerance for enforcing positive definiteness (in the final posdefify step when do2eigen is TRUE).
maxit	maximum number of iterations allowed.
trace	logical or integer specifying if convergence monitoring should be traced.

Details

This implements the algorithm of Higham (2002), and then (if do2eigen is true) forces positive definiteness using code from posdefify. The algorithm of Knol and ten Berge (1989) (not implemented here) is more general in that it allows constraints to (1) fix some rows (and columns) of the matrix and (2) force the smallest eigenvalue to have a certain value.

Note that setting corr = TRUE just sets diag(.) <- 1 within the algorithm.

Higham (2002) uses Dykstra's correction, but the version by Jens Oehlschlägel did not use it (accidentally), and still gave reasonable results; this simplification, now only used if doDykstra = FALSE, was active in nearPD() up to Matrix version 0.999375-40.

Value

If only.values = TRUE, a numeric vector of eigenvalues of the approximating matrix; Otherwise, as by default, an S3 object of class "nearPD", basically a list with components

mat	a matrix of class dpoMatrix, the computed positive-definite matrix.
eigenvalues	numeric vector of eigenvalues of mat.
corr	logical, just the argument corr.
normF	the Frobenius norm (norm(x-X, "F")) of the difference between the original and the resulting matrix.
iterations	number of iterations needed.
converged	logical indicating if iterations converged.

Author(s)

Jens Oehlschlägel donated a first version. Subsequent changes by the Matrix package authors.

References

Cheng, Sheung Hun and Higham, Nick (1998) A Modified Cholesky Algorithm Based on a Symmetric Indefinite Factorization; SIAM J. Matrix Anal.\ Appl., 19, 1097–1110.

Knol DL, ten Berge JMF (1989) Least-squares approximation of an improper correlation matrix by a proper one. Psychometrika 54, 53–61.

Higham, Nick (2002) Computing the nearest correlation matrix - a problem from finance; IMA Journal of Numerical Analysis 22, 329–343.

See Also

A first version of this (with non-optional corr=TRUE) has been available as nearcor(); and more simple versions with a similar purpose posdefify(), both from package sfsmisc.

Examples

set.seed(27)
m <- matrix(round(rnorm(25),2), 5, 5)
m <- m + t(m)
diag(m) <- pmax(0, diag(m)) + 1
(m <- round(cov2cor(m), 2))

near.m <- nmNearPD(m)
round(near.m, 2)
norm(m - near.m) # 1.102 / 1.08

round(nmNearPD(m, only.values=TRUE), 9)

## A longer example, extended from Jens' original,
## showing the effects of some of the options:

pr <- matrix(c(1,     0.477, 0.644, 0.478, 0.651, 0.826,
               0.477, 1,     0.516, 0.233, 0.682, 0.75,
               0.644, 0.516, 1,     0.599, 0.581, 0.742,
               0.478, 0.233, 0.599, 1,     0.741, 0.8,
               0.651, 0.682, 0.581, 0.741, 1,     0.798,
               0.826, 0.75,  0.742, 0.8,   0.798, 1),
               nrow = 6, ncol = 6)

nc  <- nmNearPD(pr)

nlmixr2est documentation built on Oct. 8, 2023, 9:06 a.m.