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funrar package

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:

Violle C., Thuiller W., Mouquet N., Munoz F., Kraft NJB, Cadotte MW, Livingstone SW, Mouillot D., Functional Rarity: The Ecology of Outliers, Trends in Ecology & Evolution, Volume 32, Issue 5, May 2017, Pages 356-367, ISSN 0169-5347, https://doi.org/10.1016/j.tree.2017.02.002.

Citation

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")

Installation

The package is on CRAN, you can install it using:

install.packages("funrar")

If you want to have the latest development version use remotes:

# install.packages("remotes") # If 'remotes' is not installed yet
remotes::install_github("Rekyt/funrar", build_vignettes = TRUE)

Example vignettes

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 vignette() abd browseVignettes() functions.

References

Rabinowitz D., Seven forms of rarity In The Biological Aspects of Rare Plant Conservation (1981), pp. 205-217

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Version

Install

install.packages('funrar')

Monthly Downloads

425

Version

1.5.0

License

GPL (>= 2)

Issues

Pull Requests

Stars

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Maintainer

Last Published

September 23rd, 2022

Functions in funrar (1.5.0)

distinctiveness_stack

Functional Distinctiveness on a stacked data.frame
distinctiveness_global

Global/Regional Functional Distinctiveness from dissimilarity matrix
distinctiveness_com

Functional Distinctiveness for a single community
distinctiveness_dimensions

Distinctiveness across combinations of traits
distinctiveness_range

Alternative Truncated Functional Distinctiveness
funrar

Compute all Functional Rarity Indices from Matrices
compute_dist_matrix

Compute a Functional Dissimilarity Matrix
distinctiveness_alt

Truncated Functional Distinctiveness
combination_trait_dist

Compute Multiple distance matrices from a single trait table
distinctiveness

Functional Distinctiveness on site-species matrix
stack_to_matrix

Stacked (= tidy) data.frame to matrix
scarcity_stack

Scarcity on a stacked data.frame
restrictedness

Geographical Restrictedness on site-species matrix
is_relative

Tell if matrix or data.frame has relative abundances
scarcity

Scarcity on site-species matrix
make_relative

Relative abundance matrix from absolute abundance matrix
funrar_stack

Compute all Functional Rarity Indices from stacked data.frames
scarcity_com

Scarcity for a single community
restrictedness_stack

Geographical Restrictedness for stacked data.frame
matrix_to_stack

Matrix to stacked (= tidy) data.frame
uniqueness

Functional Uniqueness for site-species matrix matrix
uniqueness_dimensions

Uniqueness across combinations of traits
uniqueness_stack

Functional Uniqueness on stacked data.frame