NEWS.md

In prospectr: Miscellaneous Functions for Processing and Sample Selection of Spectroscopic Data

prospectr 0.2.7 (cakes)

Improvements and fixes

• 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.

prospectr 0.2.6

Improvements and fixes

• 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.

prospectr 0.2.5

Improvements and fixes

• 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).

prospectr 0.2.4

Improvements and fixes

• 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.

prospectr 0.2.3

New features

• 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.

Improvements and fixes

• 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

Changes

• In the 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.

prospectr 0.2.2

New features

• a new function for baseline correction was added. See baseline()

Improvements and fixes

• 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)

prospectr 0.2.1

• New license
• The detrend function now allows to remove trends corresponding to different polynomial orders. Check the new 'p' argument.
• New preprocessing function: multiplicative scatter correction (msc)
• Now 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)
• Bug fix: in read_nircal(), the description file was not being properly read
• Now performing automatic unit tests with the package testthat

prospectr 0.2.0

• New maintainer [Leo Ramirez-Lopez]
• Updated vignette
• A new function (read_nircal()) for reading buchi NIRcal files has been added
• Documentation reviewed
• The description of the continuum removal algorithm is was adjusted. Previously was indicated that the implemented algorithm was based on the search for a local minimum of the absorbance spectra the algorithm, however in fact it looks for the convex hull. Thanks to Peter Tillmann for noticing this.

prospectr 0.1.4

• Fix bug in kenStone() and duplex() when the group parameter is used

prospectr 0.1.3

• Fix in DESCRITPION and NAMESPACE as required by Rcpp 0.11

prospectr 0.1.2

• bug fix for readASD() when ASD file version = 7.0
• add sanity check in spliceCorrection()

prospectr 0.1.1

• bug fix for shenkWest() when rm.outlier = TRUE
• bug fix for gapDer() when input is a data.frame

prospectr 0.1

• Initial release of the package

prospectr documentation built on June 22, 2024, 11:08 a.m.