README.md

geocmeans

An R package to perform Spatial Fuzzy C-means.

R-CMD-check

Installation

You can install a development version of the geocmeans package using the command below.

remotes::install_github(repo = "JeremyGelb/geocmeans", build_vignettes = TRUE, force = TRUE)

Authors

Jeremy Gelb, Laboratoire d’Équité Environnemental INRS (CANADA), Email: jeremy.gelb@ucs.inrs.ca

Contributors

Philippe Apparcio, Laboratoire d’Équité Environnemental INRS (CANADA), Email: philippe.apparicio@ucs.inrs.ca

About the package

Provides functions to apply Spatial Fuzzy c-means Algorithm, visualize and interpret results. This method is well suited when the user wants to analyze data with a fuzzy clustering algorithm and to account for the spatial dimension of the dataset. Indexes for measuring the spatial consistency and classification quality are proposed in addition. The algorithms were developed first for brain imagery as described in the articles of Cai and al. 2007 and Zaho and al. 2013. Gelb and Apparicio proposed to apply the method to perform a socio-residential and environmental taxonomy in Lyon (France).

Approaches for visualising uncertainty in spatial data are presented in this package. These include the three approaches developed in Lucchesi and Wikle (2017) and a fourth approach presented in Kuhnert et al. (2018).

Fuzzy classification algorithms

Four Fuzzy classification algorithms are proposed :

Each function return a membership matrix, the data used for the classification (scaled if required) and the centers of the clusters.

Parameter selections

The algorithms available require different parameters to be fixed by the user. The function selectParameters is a useful tool to compare the results of different combinations of parameters. A multicore version, selectParameters.mc, using a plan from the package future is also available to speed up the calculus.

Classification quality

Many indices of classification quality can be calculated with the function calcqualityIndexes:

Interpretation

Several functions are also available to facilitate the interpration of the classification:

Spatial inconsistency

We proposed an index to quantify the spatial inconsistency of a classification (Gelb and Apparicio). If in a classification close observations tend to belong to the same group, then the value of the index is close to 0. If the index is close to 1, then the belonging to groups is randomly distributed in space. A value higher than one can happen in the case of negative spatial autocorrelation. The index is described in the vignette adjustinconsistency. The function spatialDiag does a complete spatial diagnostic of the membership matrix resulting from a classification.

Examples

Detailed examples are given in the vignette introduction

vignette("introduction","geocmeans")

Testing

If you would like to install and run the unit tests interactively, include INSTALL_opts = "--install-tests" in the installation code.

remotes::install_github(repo = "JeremyGelb/geocmeans", build_vignettes = TRUE, force = TRUE, INSTALL_opts = "--install-tests")
testthat::test_package("geocmeans", reporter = "stop")

Contribute

To contribute to geocmeans, please follow these guidelines.

Please note that the geocmeans project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

geocmeans version 0.1.0 is licensed under GPL2 License.



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geocmeans documentation built on April 21, 2021, 9:07 a.m.