Package: MLSP
Type: Package
Title: Machine Learning Models for Soil Properties from Spectroscopy
Version: 0.2.0
Authors@R: c(
    person("Pengyuan", "Chen", role = "aut", email = "pch276@uky.edu"),
    person("Christopher", "Clingensmith", role = "aut",
           email = "c.clingensmith@ufl.edu"),
    person("Chenglong", "Ye", role = "aut", email = "chenglong.ye@uky.edu"),
    person("Sabine", "Grunwald", role = "aut", email = "sabgru@ufl.edu"),
    person("Katsutoshi", "Mizuta", role = c("aut", "cre"),
           email = "toshi.m@uky.edu"))
Description: Soil spectroscopy studies use many different combinations of
    spectral preprocessing and calibration methods, which makes results
    difficult to compare or generalize across studies. For visible and
    near-infrared (VNIR) spectra (350-2500 nm), runs every combination of
    preprocessing and calibration methods on identical repeated calibration
    and validation splits. The 26 preprocessing methods are raw reflectance,
    standard normal variate, pseudo-absorbance, and 23 Savitzky-Golay
    smoothers, first derivatives, and second derivatives with linear,
    quadratic, or cubic polynomials and 3- to 11-point windows, excluding
    settings that give mathematically identical filters. The calibration
    methods are principal component regression (PCR), partial least squares
    regression (PLSR), least absolute shrinkage and selection operator
    (LASSO), 'Cubist', and random forest. Model complexity is tuned by
    cross-validation within each calibration set, and combinations are ranked
    by the coefficient of determination (R2), root mean squared error (RMSE),
    ratio of performance to interquartile distance (RPIQ), or bias, reporting
    the top 10 by default. The methods are those most commonly used in
    published soil spectroscopy studies, following Savitzky and Golay (1964)
    <doi:10.1021/ac60214a047>, Barnes et al. (1989)
    <doi:10.1366/0003702894202201>, Rinnan et al. (2009)
    <doi:10.1016/j.trac.2009.07.007>, Bellon-Maurel et al. (2010)
    <doi:10.1016/j.trac.2010.05.006>, and Clingensmith et al. (2019)
    <doi:10.1111/ejss.12753>.
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: stats, utils, gsignal, pls, glmnet, Cubist, randomForest
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-10-20 14:44:17 UTC; root
Author: Pengyuan Chen [aut],
  Christopher Clingensmith [aut],
  Chenglong Ye [aut],
  Sabine Grunwald [aut],
  Katsutoshi Mizuta [aut, cre]
Maintainer: Katsutoshi Mizuta <toshi.m@uky.edu>
Repository: CRAN
Date/Publication: 2026-10-29 15:20:02 UTC
