Package: bipartite 2.21

Carsten F. Dormann

bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.

Authors:Carsten F. Dormann [aut, cre], Jochen Fruend [aut], Bernd Gruber [aut], Tobias Bauer [ctb], Stephen Beckett [ctb], Mariano Devoto [ctb], Gabriel M.F. Felix [ctb], Jose M. Iriondo [ctb], Tore Opsahl [ctb], Rafael B.P. Pinheiro [ctb], Rouven Strauss [ctb], Diego P. Vazquez [ctb]

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bipartite.pdf |bipartite.html✨
bipartite/json (API)

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

Bug tracker:https://github.com/biometry/bipartite/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Safariland - A pollination web from Argentina
  • barrett1987 - Individuals caught in a pollination web in boreal Canada.
  • bezerra2009 - Individuals observed in a flower-visitation network of oil-collecting bees in a Brazilian steppe.
  • elberling1999 - No. of visits in a pollination web of arctic-alpine Sweden
  • inouye1988 - A pollination network from the Snowy Mountains of New South Wales, Australia
  • junker2013 - Flower visitation network
  • kato1990 - No. of individuals caught in a pollination web of a Japanese beech forest
  • kevan1970 - A pollination network from Northern Ellesmere Island, Canada
  • memmott1999 - Flower visitation network from a meadow near Bristol, UK
  • mosquin1967 - Flower visitation network from Melville Island, Northwest Territories, Canada
  • motten1982 - A spring flower visitation network from North Carolina, USA
  • olesen2002aigrettes - A flower visitation network from the Azores
  • olesen2002flores - Another flower visitation network from the Azores
  • olito2015 - A pollination network from the Canadian Rockies
  • ollerton2003 - Ollerton2003
  • schemske1978 - A flower visitation network from Urbana, IL, USA
  • small1976 - A flower visitation network from a peat bog in Ottawa, Canada
  • vazarr - A pollination network.
  • vazcer - A pollination network.
  • vazllao - A pollination network.
  • vazmasc - A pollination network.
  • vazmasnc - A pollination network.
  • vazquec - A pollination network.
  • vazquenc - A pollination network.

On CRAN:

Conda:

cpp

10.93 score 37 stars 15 packages 592 scripts 5.7k downloads 86 mentions 80 exports 32 dependencies

Last updated 18 days agofrom:d50a93145d. Checks:1 ERROR, 11 WARNING. Indexed: yes.

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R-4.3-mac-aarch64WARNINGMar 10 2025

Exports:array2linkmxas.one.modeas.tnetBCbetalinkrbetalinkr_multibetweenness_wC.scoreCCcloseness_wclustering_tmcompartcomputeModulesconvert2moduleWebczvaluesdecimalr2dtabledegreedistrdfunDIRT_LPA_wb_plusdiscrepancyemptyendpointextinctionfcframe2websgenwebgrouplevelH2funlinklevellistModuleInformationLPA_wb_plusmetaComputeModulesmgenmodule2constraintsNDnest.smdmnestednestedcontributionnestednessnestedranknetworklevelnodespecNOSnpartitenull.distrnull.t.testnullmodelPACPDIplot.wineplotmatrixplotModuleWebplotPACplotwebplotweb2printoutModuleInformationprojecting_tmr2dexternalrestrictednullrobustnesssecond.extinctshuffle.webslope.bipartitesortmatrixsortwebspecieslevelspectral.radiusstrengthswap.websymmetrise_wtnet_igraphtogethernessV.ratiovaznullvaznullexternalversionlogviswebweb2edgeswebs2arraywine

Dependencies:cliclustercodacorpcorcpp11dotCall64fansifieldsglueigraphlatticelifecyclemagrittrmapsMASSMatrixmgcvnetworknlmepermutepillarpkgconfigRcpprlangsnaspamstatnet.commontibbleutf8vctrsveganviridisLite

Readme and manuals

Help Manual

Help pageTopics
Analysis of bipartite ecological websbipartite-package bipartite
Reshape a webarray to a web X link matrixarray2linkmx
Conversion of a network matrixas.one.mode
Ensures that networks conform to the tnet stardardsas.tnet
Individuals caught in a pollination web in boreal Canada.barrett1987
Calculate network dissimilarity (beta diversity) and its componentsbetalinkr betalinkr_multi
Betweenness centrality in a weighted networkbetweenness_w
Individuals observed in a flower-visitation network of oil-collecting bees in a Brazilian steppe.bezerra2009
Calculates the (normalised) mean number of checkerboard combinations (C-score) in a matrixC.score
Closeness centrality in a weighted networkcloseness_w
Redefined clustering coefficient for two-mode networksclustering_tm
Detects compartmentscompart
computeModulescomputeModules metaComputeModules readModuleData
Computes c and z for network modulesczvalues
Generates matrix with same marginal totals for non-negative decimal valuesdecimalr2dtable
Fits functions to cumulative degree distributions of both trophic levels of a network.degreedistr
Calculates standardised specialisation index d' (d prime) for each species in the lower trophic level of a bipartite network.dfun
Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"convert2moduleWeb DIRT_LPA_wb_plus LPA_wb_plus
Calculates discrepancy of a matrixdiscrepancy
Distance in a weighted networkdistance_w
No. of visits in a pollination web of arctic-alpine Swedenelberling1999
Deletes empty rows and columns from a matrix.empty
Computes end-point degrees for a bipartite networkendpoint
Simulates extinction of a species from a bipartite networkextinction
Calculates the functional complementarity for the rows of a webfc fd
Converts a table of observations into a network matrixedgelist2webs frame2webs
Generate a random bipartite webgenweb
Analysis of bipartite webs at the level of each of the two levels (groups) of the networkgrouplevel one.grouplevel
Specialisation of a bipartite web.H2fun
A pollination network from the Snowy Mountains of New South Wales, Australiainouye1988
Flower visitation networkjunker2013
No. of individuals caught in a pollination web of a Japanese beech forestkato1990
A pollination network from Northern Ellesmere Island, Canadakevan1970
Indices of a bipartite network at the link levellinklevel
listModuleInformationlistModuleInformation
Flower visitation network from a meadow near Bristol, UKmemmott1999
Generate simulated network according to a given probability matrixmgen
Class "moduleWeb"moduleWeb-class
Flower visitation network from Melville Island, Northwest Territories, Canadamosquin1967
A spring flower visitation network from North Carolina, USAmotten1982
Normalised degree, betweenness and closeness centralityBC CC ND
Computes nestedness of a matrix as WNODA (and NODF and WNODF)module2constraints nest.smdm NODF WNODA WNODF
Calculates any of several measures of nestednessnested
Calculates the per-species contribution to nestedness (z-score relative to null model)nestedcontribution
Calculates nestedness temperature of presence/absence matricesnestedness
Calculates the rank of a species in a matrix sorted for maximum nestednessnestedrank
Analysis of bipartite webs at the level of the entire networknetworklevel
Calculates the node-based specialisation indexnodespec
Calculates the node overlap and separation according to Strona & Veech (2015)NOS
Computes indices for a masked-one-mode networknpartite
Null model based on fitted marginal distributionnull.distr
Compares observed pattern to random webs.null.t.test
Generates null models for network analysisnullmodel
A flower visitation network from the Azoresolesen2002aigrettes
Another flower visitation network from the Azoresolesen2002flores
A pollination network from the Canadian Rockiesolito2015
ollerton2003ollerton2003
Potential for Apparent CompetitionPAC
Paired Differences IndexPDI
Plot a matrix organised by topologyplotmatrix
plotModuleWebaddEmptyColToMatrix addEmptyRowToMatrix drawModules getModuleCoordinates isCorrectModuleWebObject plotModuleWeb prepareWebForPlottingModules
Function to draw a circular plot to visualise potential apparent competition (PAC)plotPAC
Visualize a bipartite interaction matrix (e.g. a foodweb)plotweb
Visualize a tripartite interaction matrix (e.g. a tritrophic foodweb)plotweb2
printoutModuleInformationprintoutModuleInformation
Projecting binary and weighted two-mode networks onto weighted one-mode networks.projecting_tm
Generates null models for network analysis by considering external abundancesr2dexternal vaznullexternal
The restricted null model accounting for modules with nested entriesPosteriorProb restrictednull
Robustness to species extinctionsrobustness
A pollination web from ArgentinaSafariland
A flower visitation network from Urbana, IL, USAschemske1978
Secondary extinctions in bipartite networkssecond.extinct
Shuffle web entriesshuffle.web
Slope of extinction simulationslope.bipartite
A flower visitation network from a peat bog in Ottawa, Canadasmall1976
Organise matrix by topologysortmatrix
Function to sort bipartite webssortweb
Calculate various indices for network properties at the species levelspecieslevel
Calculates the spectral radius as a nestedness measurement of a bipartite matrix, possibly with regard to mass actionmassaction spectral.radius
Computes species strength according to either of two definitionsstrength
Creates null model for bipartite networksswap.web
Symmetrise_wsymmetrise_w
Exports a tnet network to an igraph objecttnet_igraph
Calculates the number of identical co-presences and co-absences for species-on-islandstogetherness
Calculates the variance-ratio as suggested by Schluter (1984)V.ratio
A pollination network.vazarr
A pollination network.vazcer
A pollination network.vazllao
A pollination network.vazmasc
A pollination network.vazmasnc
Null model with constrained connectance and moderately constrained marginal totalsvaznull
A pollination network.vazquec
A pollination network.vazquenc
Examples for some analysesconfint intasymm intereven mlik netstats plotmat quant2bin sortmatr sortmatrext vazquez.example
Log of bipartite versions and changesversionlog
Plotting function to visualize a bipartite food webvisweb
Conversion of a network matrix into a (weighted) edge listweb2edges
Puts two or more webs into one array of webswebs2array
Weighted-Interaction Nestedness Estimatorplot.wine wine