Package: funrar 1.5.0

Matthias Grenié

funrar: Functional Rarity Indices Computation

Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.

Authors:Matthias Grenié [aut, cre], Pierre Denelle [aut], Caroline Tucker [aut], François Munoz [ths], Cyrille Violle [ths]

funrar_1.5.0.tar.gz
funrar_1.5.0.zip(r-4.7)funrar_1.5.0.zip(r-4.6)funrar_1.5.0.zip(r-4.5)
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funrar_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
funrar/json (API)

# Install 'funrar' in R:
install.packages('funrar', repos = c('https://frbcesab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rekyt/funrar/issues

Pkgdown/docs site:https://rekyt.github.io

On CRAN:

Conda:

ecological-modelsecologyraritytraits

8.25 score 17 stars 2 packages 288 scripts 370 downloads 1 mentions 25 exports 3 dependencies

Last updated from:bf8a1ed53e. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK141
source / vignettesOK168
linux-release-x86_64OK131
macos-release-arm64OK144
macos-oldrel-arm64OK118
windows-develOK102
windows-releaseOK97
windows-oldrelOK89
wasm-releaseOK127

Exports:compute_dist_matrixdistinctivenessdistinctiveness_altdistinctiveness_comdistinctiveness_dimensionsdistinctiveness_globaldistinctiveness_rangedistinctiveness_stackdistinctiveness_tidyfunrarfunrar_stackmake_relativematrix_to_stackrestrictednessrestrictedness_stackrestrictedness_tidyscarcityscarcity_comscarcity_stackscarcity_tidystack_to_matrixuniquenessuniqueness_dimensionsuniqueness_stackuniqueness_tidy

Dependencies:clusterlatticeMatrix

Other functions of interest
Compute Distinctiveness from Global Pool - distinctiveness_global() | Compute functional rarity indices across combinations of traits | Compare Distinctiveness computed on all traits and each trait - distinctiveness_dimensions() | Compare Uniqueness computed on all traits and each trait - uniqueness_dimensions() | Compute Relative Abundances - make_relative()
Rendered fromother_functions.Rmdusingknitr::rmarkdown

Last update: 2022-09-23
Started: 2022-09-23

Introduction to funrar through an example
Introduction | Framework | Dataset example | Functional rarity indices | Inputs of functions | Indices | Distance matrix computation | Functional Distinctiveness computation | Formula | Computation with site-species matrix | Computation with stacked data.frame | Scarcity | Computation | Uniqueness | Geographical Restrictedness | funrar | Plots | References
Rendered fromfunrar.Rmdusingknitr::rmarkdown

Last update: 2022-09-01
Started: 2022-09-01

Sparse Matrices within funrar
Sparse Matrices Usefulness | Benchmark | Systematic benchmark
Rendered fromsparse_matrices.Rmdusingknitr::rmarkdown

Last update: 2022-09-01
Started: 2016-07-06

Alternative Distinctiveness definition
Presence-Absence | Theoretical definition | Implementation | Using real data | Considering Abundance | Definitive formula | Reconciling with presence-absence definition
Rendered fromnew_distinctiveness.Rmdusingknitr::rmarkdown

Last update: 2022-08-30
Started: 2018-08-04

Readme and manuals

Help Manual

Help pageTopics
Compute Multiple distance matrices from a single trait tablecombination_trait_dist
Compute a Functional Dissimilarity Matrixcompute_dist_matrix distance_matrix
Functional Distinctiveness on site-species matrixdistinctiveness
Truncated Functional Distinctivenessdistinctiveness_alt
Functional Distinctiveness for a single communitydistinctiveness_com
Distinctiveness across combinations of traitsdistinctiveness_dimensions
Global/Regional Functional Distinctiveness from dissimilarity matrixdistinctiveness_global
Alternative Truncated Functional Distinctivenessdistinctiveness_range
Functional Distinctiveness on a stacked data.framedistinctiveness_stack distinctiveness_tidy
Compute all Functional Rarity Indices from Matricesfunrar
Compute all Functional Rarity Indices from stacked data.framesfunrar_stack
Tell if matrix or data.frame has relative abundancesis_relative
Relative abundance matrix from absolute abundance matrixmake_relative
Matrix to stacked (= tidy) data.framematrix_to_stack matrix_to_tidy
Geographical Restrictedness on site-species matrixrestrictedness
Geographical Restrictedness for stacked data.framerestrictedness_stack restrictedness_tidy
Scarcity on site-species matrixscarcity
Scarcity for a single communityscarcity_com
Scarcity on a stacked data.framescarcity_stack scarcity_tidy
Stacked (= tidy) data.frame to matrixstack_to_matrix tidy_to_matrix
Functional Uniqueness for site-species matrix matrixuniqueness
Uniqueness across combinations of traitsuniqueness_dimensions
Functional Uniqueness on stacked data.frameuniqueness_stack uniqueness_tidy