Package: bipartite 2.20

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], 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'))

Peer review:

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:

11.61 score 35 stars 15 packages 572 scripts 4.1k downloads 86 mentions 79 exports 31 dependencies

Last updated 4 months agofrom:ae02e38066. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-win-x86_64NOTENov 12 2024
R-4.5-linux-x86_64NOTENov 12 2024
R-4.4-win-x86_64OKNov 12 2024
R-4.4-mac-x86_64OKNov 12 2024
R-4.4-mac-aarch64OKNov 12 2024
R-4.3-win-x86_64OKNov 12 2024
R-4.3-mac-x86_64OKNov 12 2024
R-4.3-mac-aarch64OKNov 12 2024

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

Dependencies:cliclustercodacpp11dotCall64fansifieldsglueigraphlatticelifecyclemagrittrmapsMASSMatrixmgcvnetworknlmepermutepillarpkgconfigRcpprlangsnaspamstatnet.commontibbleutf8vctrsveganviridisLite

Starting with bipartite

Rendered fromIntro2bipartite.Rnwusingutils::Sweaveon Nov 12 2024.

Last update: 2023-12-03
Started: 2018-03-18

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
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