loocv {OmicsPLS}

K fold CV for O2PLS

Description

For (a grid of) values for a, nx and ny, loocv estimates the prediction error using k-fold CV.

Usage

loocv(
  X,
  Y,
  a = 1:2,
  a2 = 1,
  b2 = 1,
  fitted_model = NULL,
  func = o2m,
  app_err = F,
  kcv,
  stripped = TRUE,
  p_thresh = 3000,
  q_thresh = p_thresh,
  tol = 1e-10,
  max_iterations = 100
)

Arguments

X

Numeric matrix. Vectors will be coerced to matrix with as.matrix (if this is possible)

Y

Numeric matrix. Vectors will be coerced to matrix with as.matrix (if this is possible)

a

Vector of integers. Contains the numbers of joint components.

a2

Vector of integers. Contains the numbers of orthogonal components in X.

b2

Vector of integers. Contains the numbers of orthogonal components in Y.

fitted_model

List. Deprecated. O2PLS model fit with o2m. Is used to calculate the apparent error without recalculating this fit.

func

Function to fit the O2PLS model with. Only o2m and o2m_stripped are supported.

app_err

Logical. Deprecated. Should the apparent error also be computed?

kcv

Integer. The value of k, i.e. the number of folds. Choose N for LOO-CV.

stripped

Logical. Use the stripped version of o2m (usually when cross-validating)?

p_thresh

Integer. If X has more than p_thresh columns, a power method optimization is used, see o2m2

q_thresh

Integer. If Y has more than q_thresh columns, a power method optimization is used, see o2m2

tol

Double. Threshold for which the NIPALS method is deemed converged. Must be positive.

max_iterations

Integer. Maximum number of iterations for the NIPALS method.

Details

Note that this function can be easily parallelized (on Windows e.g. with the parallel package.).

The parameters a, a2 and b2 can be integers or vectors of integers. A for loop is used to loop over all combinations. The resulting output is a list, which is more easy to interpret if you use array(unlist(output_of_loocv$CVerr)) as in the example below. The array wil have varying a along the first dimension and a2 and b2 along the second and third respectively. Typing example(loocv) (hopefully) clarifies this function.

Value

List with two numeric vectors:

CVerr

Contains the k-fold CV estimated RMSEP

Fiterr

Contains the apparent error