feemsplithalf: Split-half analysis of PARAFAC models

In albatross: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices

Split-half analysis of PARAFAC models

Description

This function validates PARAFAC with different numbers of components by means of splitting the data cube in halves, fitting PARAFAC to them and comparing the results DeSarbo1984.

Usage

  feemsplithalf(
    cube, nfac, splits, random, groups, fixed, ..., progress = TRUE
  )
  ## S3 method for class 'feemsplithalf'
plot(
    x, kind = c('tcc', 'factors', 'aggtcc', 'bandfactors'), ...
  )
  ## S3 method for class 'feemsplithalf'
print(x, ...)
  ## S3 method for class 'feemsplithalf'
coef(
    object, kind = c('tcc', 'factors', 'aggtcc', 'bandfactors'), ...
  )

Arguments

cube	A feemcube object.
nfac	An integer vector of numbers of factors to check.
splits	A scalar or a two-element vector consisting of whole numbers. The first element is the number of parts to split the data cube into, which must be even. After splitting, the parts are recombined into non-intersecting halves Murphy2013, which are subjected to PARAFAC decomposition and compared against each other. The second element, if specified, limits the total number of comparisons between the pairs, since the number of potential ways to recombine the parts of the data cube into halves grows very quickly. The number of PARAFAC models fitted is 3{ 2 \cdot \mathtt{splits[2]}

2 * splits[2] 2 &middot; <code>splits[2]</code>. If only splits[1] is specified, splits[2] defaults to \mathtt{splits[1]} \choose {\mathtt{splits[1]}/2} .

Mutually incompatible with the parameters random, fixed.

Details

As the models (loadings 3{\mathbf A

Value

feemsplithalf, print.feemsplithalf

An object of class feemsplithalf, containing named fields:

factors

A list of feemparafac objects containing the factors of the halves. The list has dimensions, the first one corresponding to the halves (always 2), the second to different numbers of factors (as many as in nfac) and the third to different groupings of the samples (depends on splits or random).

tcc

A named list containing arrays of Tucker's congruence coefficients between the halves. Each entry in the list corresponds to an element in the nfac argument. The dimensions of each array in the list correspond to, in order: the factors (1 to nfac[i]), the modes (emission or excitation) and the groupings of the samples (depending on splits or random).

nfac

A copy of nfac argument.

plot.feemsplithalf

A lattice plot object. Its print or plot method will draw the plot on an appropriate plotting device.

coef.feemsplithalf

A data.frame containing various columns, depending on the value of the kind argument:

tcc

factor

The factor (out of nfac) under consideration.

tcc

Tucker's congruence coefficient between a pair of matching components. Out of two possible values (TCC between excitation loadings or emission loadings), the minimal one is chosen, because the same rule is used to find which components match when reordering them in a pair of models.

test

The sequence number for each pair of models in the split-half test, related to the third dimension of object$factors or object$tcc. May be used to group values for plotting or aggregation.

subset

Consists of two-element lists containing indices of the samples in each half of the original cube.

nfac

The number of factors in the pair of models under consideration.

factors

wavelength

Emission and excitation wavelengths.

value

The values of the loadings.

factor

Number of the factor, 1 to nfac.

mode

The mode the loading value belongs to, “Emission” or “Excitation”.

nfac

Total number of factors.

test

Sequence number of a split-half test, indicating a given way to split the dataset in a group of splits with the same numbers of factors.

half

Number of the half, 1 or 2.

subset

For every row, this is an integer vector indicating the subset of the original data cube that the loadings have been obtained from.

aggtcc

The columns tcc, nfac, test after aggregation of coef(kind = 'tcc').

bandfactors

Columns wavelength, factor, mode, nfac from coef(kind = 'factors'), plus columns lower, estimate, upper signifying the outputs from the aggregation function.

References

\bibliography

See Also

feemparafac, parafac, congru, feemcube.

Examples

  data(feems)
  cube <- feemscale(feemscatter(cube, rep(14, 4)), na.rm = TRUE)

  (sh <- feemsplithalf(
    cube, 1:4, splits = 4, # => S4C6T3
    # splits = c(4, 2) would be S4C4T2, and so on
    # the rest is passed to multiway::parafac;
    ctol = 1e-4
    # here we set a mild stopping criterion for speed;
    # be sure to use a stricter one for real tasks
  ))

  # specifying fixed halves to compare as list of 2-element lists
  fixed <- list(
    list(1:6, 7:12),
    list(seq(1, 11, 2), seq(2, 12, 2))
  )
  sh.f <- feemsplithalf(cube, 2:3, fixed = fixed, ctol = 1e-4)

  plot(sh, 'aggtcc')
  head(coef(sh, 'factors'))

albatross documentation built on May 29, 2024, 9:10 a.m.