Package: fundiversity 1.1.1.9000

fundiversity: Easy Computation of Functional Diversity Indices

Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).

Authors:Matthias Grenié [aut, cre], Hugo Gruson [aut]

fundiversity_1.1.1.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fundiversity/json (API)

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

Bug tracker:https://github.com/funecology/fundiversity/issues

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

Datasets:
  • site_sp_birds - Site-species matrix of birds along a Tropical Gradient
  • site_sp_plants - Site-species matrix of plants along a Tropical Gradient
  • traits_birds - Functional Traits of Frugivorous Birds along a Tropical Gradient
  • traits_plants - Functional Traits of Fleshy-fruit plants along a Tropical Gradient

On CRAN:

Conda:

biodiversitybiodiversity-indicatorsbiodiversity-informaticsfunctional-diversityfunctional-ecologyfunctional-traitfunctional-traitstraittrait-basedtraits

8.12 score 43 stars 1 packages 51 scripts 451 downloads 6 exports 22 dependencies

Last updated from:0a65df73e2. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK148
source / vignettesOK170
linux-release-x86_64OK143
macos-release-arm64OK104
macos-oldrel-arm64OK160
windows-develOK110
windows-releaseOK126
windows-oldrelOK110
wasm-releaseOK143

Exports:fd_fdisfd_fdivfd_fevefd_fricfd_fric_intersectfd_raoq

Dependencies:abindclustercodetoolsdigestfuturefuture.applygeometryglobalslatticelinproglistenvlpSolvemagicMASSMatrixmgcvnlmeparallellypermuteRcppRcppProgressvegan

Parallelize Computation of Indices
Running code in parallel | Performance comparison
Rendered fromfundiversity_1-parallel.Rmdusingknitr::rmarkdown

Last update: 2026-03-30
Started: 2022-11-08

Performance Benchmark with other packages
Other packages to compute FD indices | Main functions | Benchmark between packages | Functional Dispersion (FDis) | Functional Divergence (FDiv) | Functional Evenness (FEve) | Functional Richness (FRic) | Functional Richness Intersection (FRic_intersect) | Rao's Quadratic Entropy (Q) | Benchmark within fundiversity | Increasing the number of species | Functional Richness | Functional Divergence | Rao's Quadratic Entropy | Functional Evenness | Comparing between indices | Increasing the number of sites | References
Rendered fromfundiversity_2-performance.Rmdusingknitr::rmarkdown

Last update: 2026-03-30
Started: 2022-11-08

Overview of how to use fundiversity
Required data | Functional Richness (FRic) - fd_fric() | Functional volume intersect (FRic_intersect) - fd_fric_intersect() | Functional Divergence (FDiv) - fd_fdiv() | Functional Evenness (FEve) - fd_feve() | Functional Dispersion (FDis) - fd_fdis() | Rao's Quadratic Entropy (Q) - fd_raoq() | Large site-species data / sparse matrices | Standardizing trait data | Non-continuous traits? | Missing values in traits? | Functions summary table | References
Rendered fromfundiversity.Rmdusingknitr::rmarkdown

Last update: 2024-04-03
Started: 2020-12-20

Check Numerical Correctness of Indices
Changes of abundance | Changes of coordinates (= traits)
Rendered fromfundiversity_3-correctness.Rmdusingknitr::rmarkdown

Last update: 2022-12-19
Started: 2022-11-08

Design Principles for fundiversity
Scope | Dependencies | Functions | Each index should be computed in its own separate function | Input data should not be transformed without any explicit action from the user | Inputs | Outputs | Functions should output data.frames | The outputs of functions should be similar in structure
Rendered fromfundiversity_4-design-principles.Rmdusingknitr::rmarkdown

Last update: 2022-11-08
Started: 2022-11-08