Package: mFD 1.0.7.9000

mFD: Compute and Illustrate the Multiple Facets of Functional Diversity

Computing functional traits-based distances between pairs of species for species gathered in assemblages allowing to build several functional spaces. The package allows to compute functional diversity indices assessing the distribution of species (and of their dominance) in a given functional space for each assemblage and the overlap between assemblages in a given functional space, see: Chao et al. (2018) <doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>, Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al. (2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009) <doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included. Visit the 'mFD' website for more information, documentation and examples.

Authors:Camille Magneville [aut, cre, cph], Nicolas Loiseau [aut], Camille Albouy [aut], Nicolas Casajus [aut], Thomas Claverie [aut], Arthur Escalas [aut], Fabien Leprieur [aut], Eva Maire [aut], David Mouillot [aut], Sebastien Villeger [aut]

mFD_1.0.7.9000.tar.gz
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mFD.pdf |mFD.html✨
mFD/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/cmlmagneville/mfd/issues

Datasets:

On CRAN:

7.23 score 25 stars 56 scripts 839 downloads 36 exports 141 dependencies

Last updated 4 months agofrom:1a82d80997. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-winOKNov 23 2024
R-4.5-linuxOKNov 23 2024
R-4.4-winOKNov 23 2024
R-4.4-macOKNov 23 2024
R-4.3-winOKNov 23 2024
R-4.3-macOKNov 23 2024

Exports:alpha.fd.fealpha.fd.fe.plotalpha.fd.hillalpha.fd.multidimalpha.multidim.plotasb.sp.summarybackground.plotbeta.fd.hillbeta.fd.multidimbeta.multidim.plotdist.nearneighbdist.pointdist.to.dffdis.plotfdiv.plotfeve.plotfide.plotfnnd.plotfori.plotfric.plotfspe.plotfunct.distfunct.space.plotfusemst.computationpanels.to.patchworkpool.plotquality.fspacesquality.fspaces.plotsp.filtersp.to.fesp.tr.summarytr.cont.fspacetr.cont.scaletraits.faxes.corvertices

Dependencies:abindade4apebackportsbase64encbetapartbootbroombslibcachemcarcarDatacheckmatecliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkdata.tabledendextendDerivdigestdoBydoSNOWdplyrDTellipseemmeansestimabilityevaluateFactoMineRfansifarverfastmapfastmatchFDflashClustfontawesomeforeachforeignFormulafsGAgawdisgenericsgeometryggplot2ggrepelgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelinproglme4lpSolvemagicmagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminpack.lmminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpatchworkpbkrtestpermutepicantepillarpixmappkgconfigplyrpromisespurrrquantregR6rappdirsrcddRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressreshape2rlangrmarkdownrpartrstatixrstudioapisassscalesscatterplot3dsnowspSparseMstringistringrsurvivaltibbletidyrtidyselecttinytexutf8vctrsveganviridisviridisLitewithrxfunyaml

Compute and Interpret Quality of Functional Spaces

Sebastien Villeger

Rendered fromCompute_and_interpret_quality_of_functional_spaces.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2022-02-11
Started: 2021-01-20

Compute Functional Diversity Hill Indices

Sebastien Villeger

Rendered fromCompute_functional_hill_indices.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2021-10-26
Started: 2021-02-10

Continuous Traits Framework

Camille Magneville

Rendered fromContinuous_traits_framework.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2023-02-20
Started: 2021-01-19

Customised plots

Camille Magneville

Rendered fromCustomised_plots.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2022-10-26
Started: 2022-10-26

How to Deal With Functional Entities

Camille Magneville

Rendered fromHow_to_deal_with_Functional_Entities.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2022-11-28
Started: 2021-01-20

mFD: General Workflow

Camille Magneville

Rendered frommFD_general_workflow.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-07-11
Started: 2021-01-19

Readme and manuals

Help Manual

Help pageTopics
Compute the set of indices based on number of species in Functional Entitiesalpha.fd.fe
Illustrate Functional Diversity indices based on Functional Entitiesalpha.fd.fe.plot
Compute Functional alpha-Diversity indices based on Hill Numbersalpha.fd.hill
Compute a set of alpha functional indices for a set of assemblagesalpha.fd.multidim
Plot functional space and chosen functional indicesalpha.multidim.plot
Summarize Assemblage x Species data frameasb.sp.summary
Plot background of multidimensional plotsbackground.plot
Dataset: Baskets Composition in Fruits Speciesbaskets_fruits_weights
Compute Functional beta-Diversity indices based on Hill Numbersbeta.fd.hill
Compute Functional beta-Diversity indices for pairs of assemblages in a multidimensional spacebeta.fd.multidim
Illustrate Functional beta-Diversity indices for pairs of assemblages in a multidimensional spacebeta.multidim.plot
Compute distance of a given point to its nearest neighbor in the functional space and the identity of the nearest neighbordist.nearneighb
Compute distances of all points to a given point in the functional spacedist.point
Merge distance object(s) into a single data framedist.to.df
Plot FDis indexfdis.plot
Plot FDiv indicefdiv.plot
Plot FEve indexfeve.plot
Plot FIde indexfide.plot
Plot FNND indexfnnd.plot
Plot FOrifori.plot
Plot FRic indexfric.plot
Dataset: Traits Values of Fruits Speciesfruits_traits
Dataset: Fruits Traits Informationsfruits_traits_cat
Plot FSpefspe.plot
Compute functional distance between speciesfunct.dist
Plot species position in a functional spacefunct.space.plot
Compute FUSE (Functionally Unique, Specialized and Endangered)fuse
Compute the Minimum Spanning Tree (MST) linking species of a given assemblagemst.computation
Plot individual plots along a pair of functional axes into a unique graphpanels.to.patchwork
Plot species from the poolpool.plot
Compute functional spaces and their qualityquality.fspaces
Plot functional space quality with a chosen quality metricquality.fspaces.plot
Retrieve information about species in a given assemblagesp.filter
Compute Functional Entities composition based on a Species x Traits matrixsp.to.fe
Summarize Species x Traits data framesp.tr.summary
Build a functional space based on continuous traits onlytr.cont.fspace
Scale continuous traitstr.cont.scale
Correlation between Traits and Axestraits.faxes.cor
Compute vertices of the Minimal Convex Hull shaping species from a single assemblage in a multidimensional functional spacevertices