MLSP 0.2.0

New features

ml_f() now compares every combination of preprocessing and calibration method in one call. By default it runs all 26 distinct preprocessing methods (raw reflectance, standard normal variate, absorbance, and Savitzky-Golay smoothing, first and second derivatives) with PCR, PLSR, LASSO, ‘Cubist’, and random forest, and returns the top 10 combinations. New arguments models, top_n, rank_by, and verbose; smoother_selection accepts "all", method names, or a function.
26 preprocessing methods are available and compared by default: raw reflectance, SNV, log10(1/R), and 23 Savitzky-Golay filters (linear and quadratic smoothers, quadratic and cubic first derivatives, and quadratic second derivatives with 3- to 11-point windows).
The 14 Savitzky-Golay settings of version 0.1.0 that reproduce another method exactly (cubic smoothers, linear first derivatives, cubic second derivatives, and the 3-point quadratic smoother) were removed; requesting one of them names the identical method to use instead.
New preprocess_methods() lists the methods and explains how window size, polynomial order, and derivative order work. The methods and naming follow Clingensmith et al. (2019), doi:10.1111/ejss.12753.
New spectral_preprocess() applies any method by name.
merge_of_lab_and_spectrum() accepts any number of soil property columns and gains soil_id, spec_id, n_splits, and cal_prop arguments.
type_of_soil accepts a column name as well as an index.

Savitzky-Golay preprocessing failed with current versions of ‘gsignal’ (named spectra are no longer passed to gsignal::sgolayfilt()).
Quadratic smoothing with 9- and 11-point windows returned the wrong object.
PCR and PLSR predictions used all components at once, giving invalid metrics; the number of components is now chosen by cross-validation (one-standard-error rule) and reported in the LV column.
Calibration metrics are now cross-validated for every model (out-of-bag for random forest); the cal-mse and cal-rpiq columns are renamed cv-mse and cv-rpiq.
Random forest results were mislabelled by number of trees; rf_ntree (default 500) now sets the number of trees.
msd.comp() no longer warns when predictions are constant.

Maintainer changed to Katsutoshi Mizuta.
All examples run on simulated spectra.
Added a ‘testthat’ test suite covering every preprocessing method and the bug fixes above.