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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.

Bug fixes

• 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.

Other changes

• 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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.