Package: fundiversity 1.1.1

Matthias Grenié

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]

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fundiversity.pdf |fundiversity.html✨
fundiversity/json (API)
NEWS

# Install 'fundiversity' in R:

install.packages('fundiversity', repos = c('https://bisaloo.r-universe.dev', 'https://cloud.r-project.org'))

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

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:

biodiversity biodiversity-indicators biodiversity-informatics functional-diversity functional-ecology functional-trait functional-traits trait trait-based traits

7.43 score 32 stars 37 scripts 419 downloads 6 exports 22 dependencies

Last updated 4 months agofrom:ee995de800. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 12 2024
R-4.5-win	OK	Nov 12 2024
R-4.5-linux	OK	Nov 12 2024
R-4.4-win	OK	Nov 12 2024
R-4.4-mac	OK	Nov 12 2024
R-4.3-win	OK	Nov 12 2024
R-4.3-mac	OK	Nov 12 2024

Exports:fd_fdis fd_fdiv fd_feve fd_fric fd_fric_intersect fd_raoq

Dependencies:abind cluster codetools digest future future.apply geometry globals lattice linprog listenv lpSolve magic MASS Matrix mgcv nlme parallelly permute Rcpp RcppProgress vegan

Overview of how to use fundiversity

Rendered fromfundiversity.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Parallelize Computation of Indices

Rendered fromfundiversity_1-parallel.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-04-03
Started: 2022-11-08

Performance Benchmark with other packages

Rendered fromfundiversity_2-performance.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-11-15
Started: 2022-11-08

Check Numerical Correctness of Indices

Rendered fromfundiversity_3-correctness.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Design Principles for fundiversity

Rendered fromfundiversity_4-design-principles.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute Functional Dispersion (FDis)	fd_fdis
Compute Functional Divergence (FDiv)	fd_fdiv
Compute Functional Evenness (FEve)	fd_feve
Compute Functional Richness (FRic)	fd_fric
Intersection between convex hulls of pairs of sites	fd_fric_intersect
Compute Rao's entropy index (Rao's Q)	fd_raoq
Options for 'fundiversity'	fundiversity-options
Site-species matrix of birds along a Tropical Gradient	site_sp_birds
Site-species matrix of plants along a Tropical Gradient	site_sp_plants
Functional Traits of Frugivorous Birds along a Tropical Gradient	traits_birds
Functional Traits of Fleshy-fruit plants along a Tropical Gradient	traits_plants