Rename functions

• Update all files to conform to the tidyverse style guide (#6).
• All functions renamed to match tidystyle. Old functions names work will be dropped after this version:
  • AggregateSpectra -> aggregate_spectra()
  • DoPreprocessing -> pretreat_spectra()
  • FilterSpectra -> filter_spectra()
  • FormatCV-> format_cv()
  • PlotSpectra()-> plot_spectra()
  • SaveModel()-> save_model()
  • TestModelPerformance()-> test_spectra()
  • TrainSpectralModel()-> train_spectra()
• "Preprocessing" has been renamed "Pretreatment" to minimize confusion with physical preprocessing of samples prior to scanning. Arguments have been renamed to reflect these changes (preprocessing is now pretreatment).
• Added more informative error message and documentation for random forest tune length (tune.length must be set to 5 when model.algorithm == "rf").
• Additional flexibility for plot_spectra() including color and title customization and the option to forgo filtering (#5).
• Named list output for all functions to enable easier access to individual elements.
• Always return model and variable importance results with train_spectra() and test_spectra().
• Add variable importance for PLSR (#9).
• Enable selection of k for k-fold cross-validation within the training set. Previously, k was fixed at 5 (#10).
• save_model() now automatically selects the best model if provided with multiple pretreatments.
• Code simplified and streamlined to facilitate future updates.
• Export predicted values as well as performance statistics for each training iteration (#11).
• wavelengths is no longer a required argument for any of the waves functions.
• The proportion of samples to include in the training set can now be selected with the argument proportion.train. Previously, this proportion was fixed at 0.7 (#13).
• Bug fix: aggregate_spectra() now allows for aggregation by a single grouping column (#14).
• The parameter save.model in the function save_model() has been renamed to write.model for clarity.