read_nircal(): The function was crashing because of some special characters
in the IDs. This has been fixed
(#65).
kenStone(): An issue has been fixed for the k argument when group
was used. The function prevented to pass a value to the k argument
larger than the number of groups passed to the group argument
(#51). Thanks to
Michael Simmler from Agroscope for pointing at this issue.
duplex(): Avoid error when the number of samples to select is exactly half
of the size of the input data set
(#48). Thanks to Philipp
Baumann for his pull request solving this issue. Some modifications to his
original solution were made which also address the concerns raised by
Matthew Dirks (skylogic004)
(#56). Thank you!
read_nircal(): fixes a bug when reading some special type of
comments of each sample in the file.
read_nircal(): non-utf characters in sample IDs are properly handled (before
some IDs were wrongly converted into NAs).Non-UTF8 characters are now converted
to their corresponding codes.
Documentation is now compatible with HTML5.
kenStone(): an error in a sanity check that prevented the
function to run when the number of groups to be selected was smaller than the
total number of groups. This sanity check has been fixed. Thanks to
Pogs Manalili for reporting this (#41).
kenStone(): this function was failing when when using the Mahalanobis distance
on a matrix of one column. By default the function transforms the matrix onto
the Mahalanobis space using either SVD or eigendecomposition. This makes sense
for matrices with more than two columns. However for a matrix of one column, we
now assume that such space is equivalent to the variable divided by the its
standard deviation. Thanks to Sergio Roldan (https://github.com/sdroldan) for
reporting this (#40).
spliceCorrection(): correcting more than one point at once (argument splice)
in the spectra was returning an error. This was a bug introduced in
version 0.2.4. Thanks to Jose Lucas Safanelli (https://github.com/zecojls)
for reporting this (#39).
baseline(): in some cases the function did not properly capture the baseline
confounding maximum values of a peaks as part of the baseline. This has been
addressed in this version by ensuring the envelope used in the computation of the
convex hull (used to extract the baseline) is properly defined. At the edges,
this envelope has always values higher than any peak of the spectrum.
read_nircal(): the function was wrongly identifying actual .nir files as
invalid. This preventing the function from reading any nir file. This has been
fixed.
The kenStone() function now includes a new feature that allows to initialize the
calibration sample search with a user-defined subset of observations (which are
to be included in the final calibration subset). Thanks to Thorsten Behrens and
Philipp Baumann for suggesting this feature.
The gap-segment derivatives (gapDer()) function now allows for high order
derivatives. In previous versions the function only allowed up to derivatives of
4th order, in this version the the function accepts as derivative order
any integer larger than 1.
binning() a bug in the creation of the binning groups has been fixed. This bug
is in fact inherited from a problem in the findInterval() function. The breaks
(given in the vec arument) might get corrupted when they contain many decimal
places. These breaks (in vec) are used to define the final bins. The problem in
the binning function was that when a frequency
variable (e.g. wavelength) was exactly on the left of the bin
range the variable was assigned to the next bin. In some cases this lead to
small discrepancies in the in the computation of the mean of the bins.
spliceCorrection() now accepts one or two values as input for the splice
argument. Previously it only accepted a vector of length two. For example, now it
corrrects for splice steps of spectra that originates from spectrometers
with two detectors (i.e. it corrects for the potential abrupt transition
betwteen the two detectors).
An extra sanity check has been added to the read_nircal() function. The
function evaluaes whether it is indeed a file properly produced by the BUCHI
nircal software.
There was a bug in the filter for the 3rd order derivative in gap segment
derivative (gapDer()) function. One of the factors in the filter had a wrong
negative sign.
There was a bug in the read_nircal() function. It emerged only in some files and
prevented the function from reading the Description field properly
msc() function the argument reference_spc has been renamed to
ref_spectrum to emphasize that its input must be is a vector and not a
matrix of spectra.baseline()The package was stripping some symbols for Rcpp functions in Makevars in order to reduce the installation size of the package. Now these lines have been commented to comply with CRAN policies
standardNormalVariate() returns now a matrix (previously a data.frame)
resample() also has a new argument (...) to pass additional arguments to the
splinefun() function (of stats) used within resample() when the argument
interpol = 'spline' (the default since version 0.2.0)read_nircal(), the description file was not being properly readread_nircal()) for reading buchi NIRcal files has been addedkenStone() and duplex() when the group parameter is usedreadASD() when ASD file version = 7.0spliceCorrection()shenkWest() when rm.outlier = TRUEgapDer() when input is a data.frame