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Archived repo (see Readme) - R package for regression and discrimination, with special focus on chemometrics and high-dimensional data.

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This repository is archived. Package rchemo has been moved to this new repository.

rchemo - Dimension reduction, Regression and Discrimination for Chemometrics

Version 0.0-18

Jchemo provides functions and pipelines for predictions in chemometrics or other domains, with focus on high dimensional data.

The package was initially about k-nearest neighbors locally weighted partial least squares regression and discrimination models (kNN-LWPLSR an kNN-LWPLSDA; e.g. Lesnoff et al 2021 https://doi.org/10.1002/cem.3209). It has now been expanded to other methods.

Generic functions such as transform, predict, coef and summary are available. Tuning the models is facilitated by functions gridscore (validation dataset) and gridcv (cross-validation), with faster versions for models based on latent variables (LVs) (gridscorelv and gridcvlv) and ridge regularization (gridscorelb and gridcvlb).

NOTE: This R package rchemo is currently only maintained. The new current and more expanded package is Jchemo in Julia language.

Available functions

Click HERE to see the list of the available functions

After the package installation, all the functions have a help page with documented examples.

News

Click HERE to see what changed in the last version

or write in the R console

news(package = "rchemo")

Dependent packages

rchemo is dependent to the following packages available on CRAN:

Package Which use in rchemo?
data.table Fast data management
FNN Fast search of nearest neighbours
signal Savitsky-Golay derivation, and signal interpolation
e1071 SVM models

Installation

Using Rstudio is recommended for installation and usage

1. Install package 'remotes' from CRAN

Use the Rstudio menu

or write in the R console

install.packages("remotes")

2. Install package 'rchemo'

a) Most recent version

Write in the R console

remotes::install_github("mlesnoff/rchemo", dependencies = TRUE, 
  build_vignettes = TRUE)

In case of the following question during installation process:

These packages have more recent versions available.
Which would you like to update?"

it is recommended to skip updates (usually choice 3 = None)

b) Any given tagged version

e.g. with tag "v1.9-0" (Be carefull, this is not the more recent version)

write in the R console

remotes::install_github("mlesnoff/rchemo@v1.9-0", dependencies = TRUE, 
  build_vignettes = TRUE)

3. Usage

Write in the R console

library(rchemo)

Author

Matthieu Lesnoff

matthieu.lesnoff@cirad.fr

How to cite

Lesnoff, M. 2021. R package rchemo: Dimension reduction, Regression and Discrimination for Chemometrics. https://github.com/mlesnoff/rchemo. CIRAD, UMR SELMET, Montpellier, France