utrechtuniversity / scca

Spectral Clustering Correspondence Analysis

SCCA: Spectral Clustering Correspondence Analysis in R

Introduction

The SCCA package implements in R the methodological approach to CA as proposed in Correspondence analysis, spectral clustering and graph embedding: applications to ecology and economic complexity van Dam et al; 2021.

Installation

The package can be installed directly from Github with the code below. Ensure the package devtools has been installed.

#install.packages("devtools")
library(devtools)
install_github("UtrechtUniversity/scca", build_vignettes = TRUE)

Documentation of exported functions and data set

After loading the package a list of all exported functions and data sets can be retrieved by ?SCCA and the documentation of an individual function by ?<function name>; e.g. ?scca_compute.

The methodology and the use of the functions and the data are explained in the included vignette. After installing package SCCA use browseVignettes('SCCA') in the R(Studio) console.

License

The software code is licensed under MIT. The next section (References) provides links to sources of the included datasets. See there for licences of those data sets.

References

Software

van Dam, Alje, Dekker, Mark, Morales-Castilla, Ignacio, Rodríguez, Miguel Á., Wichmann, David and Baudena, Mara (2021); Correspondence analysis, spectral clustering and graph embedding: applications to ecology and economic complexity; Scientific Reports; DOI: 10.1038/s41598-021-87971-9

Included data set

Faurby, Søren e.a; 2019; HYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology

The team

The team members are:

• Mathematical foundations of the code

  • Alje van Dam, Copernicus Institute of Sustainable Development and Centre for Complex Systems Studies, Utrecht University, the Netherlands
  • Mark Dekker, Department of Information and Computing Sciences and Centre for Complex Systems Studies, Utrecht University, the Netherlands

• Programming and packaging

  • Kees van Eijden Research Engineering/ITS, Utrecht University, the Netherlands

• With contributions of

  • Ignacio Morales Castilla, Global Change Ecology and Evolution Group, Department of Life Sciences, University of Alcala´, Spain
  • Jonathan de Bruin, Research Engineering/ITS, Utrecht University, the Netherlands
  • Raoul Schram, Research Engineering/ITS, Utrecht University, the Netherlands
  • Mara Baudena, National Research Council of Italy, Institute of Atmospheric Science and Climate (CNR-ISAC), Turin, Italy; Copernicus Institute of Sustainable Development and Centre for Complex Systems Studies, Utrecht University, the Netherlands

How to cite SCCA

To cite the SCCA repository and R package, use citation("SCCA") to retrieve the BibTex entry. Otherwise use the following format:

van Eijden, Kees et al; 2021; SCCA: Spectral Clustering Correspondence Analysis in R; Utrecht University; DOI: 10.5281/zenodo.4665670. Also available at Utrecht University.

Please also cite the paper van Dam et al, 2021 when using the SCCA repository.