Computes functional rarity indices as proposed by Violle et al.
funrar is a package to compute functional rarity indices, it quantifies how species are rare both from a functional and an extent point of view. Following the different facets of rarity proposed by Rabinowitz (1981). See this reference for more details on Functional Rarity indices:
NEWS: the funrar paper just got published
Please cite the following reference when using
funrar in a paper:
Grenié M, Denelle P, Tucker CM, Munoz F, Violle C. funrar: An R package to characterize functional rarity. Divers Distrib. 2017;00:1–7. https://doi.org/10.1111/ddi.12629
or refer to the CITATION file, using:
citation(package = "funrar")
The package is on CRAN, you can install it using:
If you want to have the latest development version use
# install.packages("devtools") # If 'devtools' is not installed yetdevtools::install_github("Rekyt/funrar", build_vignettes = TRUE)
Apart from base packages dependencies,
funrar depends on
In addition to code example included in help of functions, two vignettes explain how to use the package. The functional rarity indices vignette explains in details the different indices and function provided; while the sparse matrices vignette shows how to use sparse matrices to gain speed in memory when computing functional rarity indices.
Access the vignette through R using the
Rabinowitz D., Seven forms of rarity In The Biological Aspects of Rare Plant Conservation (1981), pp. 205-217
distinctiveness_dimensions()that generated errors on cran server.
stack_to_matrix(x, sparse = TRUE)(#25);
comput_dist_matrix(), as it defaults to Gower's distance (#27);
rarity_dimensions()in two more explicit functions:
distinctiveness_dimensions()split corresponding tests;
distinctiveness()now fully conserve the dimnames of the provided site-species matrix.
rarity_dimensions()now comprises both Uniqueness and Distinctiveness;
reshape2from suggested packages.
make_absolute()defunct because it was based on false assumptions and would not give back matrices of relative abundances;
distinctiveness()to compute across single communities or regional pools;
rarity_dimensions()function to measure the different facets of rarity according to the trait;
compute_dist_matrix()to scale traits before computing distance, these arguments are sensitive to the specific distance metric used;
roxygen2to generates documentation.
goodpracticeto enforce better code style,
is_relative()function to test if matrix contains relative abundances,
distinctiveness()now warns if it is not the case (#21),
microbenchmarkfollowing CRAN advices.
make_relative()and reverse function
NEWS.mdfile to track changes to the package.