tests/testthat/test-nearPd.R

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

nmTest({
  test_that("test nearPD with same functions as Matrix", {
    # https://github.com/cran/Matrix/blob/65c37738919156f6bbb682a1d8198d715a82a19f/tests/dpo-test.R#L69-L136
    # Testing nearPD() --- this is partly in  ../man/nearPD.Rd :

    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
    )

    pr <- 0.5 * (pr + t(pr))

    .npd <- function(x, conv.tol = 1e-7, ...) {
      .ret <- as.matrix(Matrix::nearPD(x, conv.tol = conv.tol, ...)$mat)
      dimnames(.ret) <- NULL
      .ret
    }

    expect_equal(nmNearPD(pr, conv.tol = 1e-7), .npd(pr))
    expect_equal(nmNearPD(pr, conv.tol = 1e-7, doDykstra = FALSE), .npd(pr, doDykstra = FALSE))
  })
})