| NEWS | R Documentation |
The const argument of feemparafac (and other
functions that call it) now defaults to non-negativity. The previous
default of an unconstrained model can be achieved by setting the
argument to NULL.
Fixed the bugs in feemjackknife and feemsplithalf
which prevented them from working with 1-component models.
Fixed the bugs preventing feem and feemcube
objects from being properly indexed by their dimnames.
The data(feems) dataset has been replaced with a
synthetic one, with perfectly matching absorbance spectra.
New function feemflame to model fluorescence and
scattering signal at the same time.
New function feemindex to calculate fluorescence indices
and named peak values used in dissolved organic matter analysis.
When the samples and the absorbance information don't match,
feemife now provides an explanation of what went wrong.
When an error happens during the processing of a feem
inside a collection (a feemcube or a list of feems) or
during feemlist file import, the offending sample (or file) is
now reported, and the error can be trapped without losing the
traceback.
The feemcube function can now return the original cube
used to fit feemparafac, feemjackknife,
feemsplithalf objects.
feem now supports text files from Edinburgh Instruments
F900 software.
feemlist can now take an importer function as an argument.
feemsplithalf can limit the number of split-combine
comparisons (the splits argument) or take a fixed list of
halves to fit and compare (the fixed argument).
HTML version of the manual now passes Tidy validation without warnings.
Fixed a bug in numerical differentiation code for
feemscatter(method = 'whittaker') that resulted in d-th
order derivatives being 2^d times smaller than they should have
been. Existing optimal lambda values will have to be updated by
dividing them by 2^(2d).
When interpolating using “loess” or “kriging” methods, predicted negative values are replaced with zeroes. Previously, this happened for the whole FEEM, but only with “loess”.
feemcube now can also extract the original cube from
feemparafac objects.
Simplified the feemlist(..., simplify.names = TRUE) logic,
hopefully preventing the test failure on some macOS machines.
Made the feem(..., 'table', fileEncoding = '...') logic
more robust, especially on older versions of R where it could still
fail when fileEncoding could not be represented in the locale
encoding.
example(write.openfluor) no longer leaves files it creates
in the per-session temporary directory.
Added a new ‘whittaker’ interpolation method for
feemscatter and feemgrid based on Whittaker smoothing
with configurable difference order(s) and optional iterative penalty
against resulting negative values. This brings in a dependency on the
recommended Matrix package.
The ‘pchip’ interpolation method now offers a choice whether to interpolate the EEM by row, by column, or to do both and average the results (thanks staRdom for the trick). It also doesn't crash anymore when trying to 1-D interpolate less than 3 defined points, falling back to linear interpolation instead.
Added feem methods for strings and connections, making
it possible to read EEMs from files in simple table formats, including
those produced by Horiba and Panorama software.
Added the feemlist generic to construct lists of
feem objects from eemR or EEM objects or vectors
of file and directory paths.
Added the groups argument to feemsplithalf,
making it possible to stratify the resulting halves according to a
given factor value.
Added the feemgrid generic to interpolate FEEM(s) on a
given wavelength grid.
Added coef methods for feemparafac,
feemsplithalf, feemjackknife returning the coefficients
and summary values (e.g. TCC for split-half) in “long”
data.frame format.
Added function write.openfluor to export a fitted
feemparafac object for the OpenFluor service.
Equations in the HTML help pages are now typeset using HTML features instead of plain ASCII.
Dependency on R >= 3.3 is now acknowledged. The
package doesn't actually pass R CMD check on prior versions
of R. Patches to lower the required R version are welcome if they
don't result in extensive rewrites.
Other documentation improvements.
Fixed a serious bug in feemsplithalf that would result
in partially overlapping splits being compared. It has been present
since v0.1-1. I apologise to any users of albatross who found
out they have been bitten by this. Steps have been taken to make sure
that other bugs like this don't still lurk in the code and to prevent
similar bugs from occurring in the future.
Potentially breaking change: feemife now accepts either
named absorbance / optical path length data exactly matching unique
names of samples, or a collection of exactly same length with either
names missing. Named collections of the same length as number of
samples which don't contain all unique sample names are going to be
rejected from now on.
Saved feemsplithalf and feemjackknife results now
should consume much less space and much less memory when loaded back.
This is achieved by saving the FEEM cube object in an environment and
only referencing it using vectors of indices instead of keeping copies
of its subsets.
New interpolation method: “kriging”. Very
resource-intensive, but results can be nicer-looking than either
loess or pchip.
More consistent progress bars for operations on collections of
feems. Scatter correction can now be run in parallel.
Minor documentation improvements.
Fixed a bug in feemjackknife and feemsplithalf,
which could manifest when rescale argument is not 3 and
loading scales are wildly different, resulting in poor approximation
for some of the modes.
Made the documentation for PARAFAC/split-half/jack-knife plots more prominent.
Made tests and examples much faster.
Made the gamma argument in marine.colours much
more useful.
Minor improvements in documentation.