Vis-NIR Spectral Analysis Wrapper
Aggregate data based on grouping variables and a user-provided functio...
Filter spectral data frame based on Mahalanobis distance
Format multiple trials with or without overlapping genotypes into trai...
Plot spectral data, highlighting outliers as identified using Mahalano...
Use provided model object to predict trait values with input dataset
Pretreat spectral data according to user-designated method
Functions renamed in waves 0.2.0
Save spectral prediction model and model performance statistics
Test the performance of spectral models
Train a model based predict reference values with spectral data
Originally designed application in the context of resource-limited plant research and breeding programs, 'waves' provides an open-source solution to spectral data processing and model development by bringing useful packages together into a streamlined pipeline. This package is wrapper for functions related to the analysis of point visible and near-infrared reflectance measurements. It includes visualization, filtering, aggregation, preprocessing, cross-validation set formation, model training, and prediction functions to enable open-source association of spectral and reference data. This package is documented in a peer-reviewed manuscript in the Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Useful links