The website of the package is available here
The stable version of
geocmeans is available on CRAN. You can install
it with the command below.
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)
Jeremy Gelb, Laboratoire d’Équité Environnemental INRS (CANADA), Email: email@example.com
Philippe Apparicio, Laboratoire d’Équité Environnemental INRS (CANADA), Email: firstname.lastname@example.org
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. In addition, indexes for measuring the spatial consistency and classification quality are proposed. 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). The methods can be applied to dataframes or to rasters.
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.
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.
Many indices of classification quality can be calculated with the
To assess the stability of the obtained clusters, a function for
bootstrap validation is proposed:
boot_group_validation. The results
can be used to verify if the obtained clusters are stable and how much
their centres vary.
Several functions are also available to facilitate the interpretation of the classification:
summarizeClusters(also accessible with the generic function
mapClusters(support polygon, points and polylines)
There is also a shiny app that can be used to go deeper in the result
interpretation. It requires the packages
Several spatial indices can be calculated to have a better spatial
understanding of the obtained clusters, like the global or local Moran I
calculated on the membership values, or the join-count-test on the most
likely group for each observation. ELSA and Fuzzy ELSA statistics can
also be calculated to identify areas with high or low multidimensional
spatial autocorrelation in the membership values. See functions
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.
Detailed examples are given in the vignette
If you would like to install and run the unit tests interactively,
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")
To contribute to
geocmeans, please follow these
Please note that the
geocmeans project is released with a Contributor
By contributing to this project, you agree to abide by its terms.
geocmeans version 0.1.0 is licensed under GPL2
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