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.

AuthorCarsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Mariano Devoto, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones
Date of publication2016-11-08 11:49:49
MaintainerCarsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
LicenseGPL
Version2.07

View on CRAN

Man pages

as.one.mode: Conversion of a network matrix

as.tnet: Ensures that networks conform to the tnet stardards

barrett1987: Individuals caught in a pollination web in boreal Canada.

betweenness_w: Betweenness centrality in a weighted network

bezerra2009: Individuals observed in a flower-visitation network of...

bipartite-package: Analysis of bipartite ecological webs

closeness_w: Closeness centrality in a weighted network

clustering_tm: Redefined clusering coefficient for two-mode networks

compart: Detects compartments

computeModules: Function "computeModules"

C.score: Calculates the (normalised) mean number of checkerboard...

czvalues: Computes c and z for network modules

degreedistr: Fits functions to cumulative degree distributions of both...

dfun: Calculates standardised specialisation index d' (d prime) for...

discrepancy: Calculates discrepancy of a matrix

distance_w: Distance in a weighted network

elberling1999: No. of visits in a pollination web of arctic-alpine Sweden

empty: Deletes empty rows and columns from a matrix.

endpoint: Computes end-point degrees for a bipartite network

extinction: Simulates extinction of a species from a bipartite network

fc: Calculates the functional complementarity for the rows of a...

frame2webs: Converts a table of observations into a network matrix

genweb: Generate a random bipartite web

grouplevel: Analysis of bipartite webs at the level of each of the two...

H2fun: Specialisation of a bipartite web.

inouye1988: A pollination network from the Snowy Mountains of New South...

junker2013: Flower visitation network

kato1990: No. of individuals caught in a pollination web of a Japanese...

kevan1970: A pollination network from Northern Ellesmere Island, Canada

linklevel: Indices of a bipartite network at the link level

listModuleInformation: Function "listModuleInformation"

memmott1999: Flower visitation network from a meadow near Bristol, UK

mgen: Generate simulated network according to a given probability...

moduleWeb-class: Class "moduleWeb"

mosquin1967: Flower visitation network from Melville Island, Northwest...

motten1982: A spring flower visitation network from North Carolina, USA

nested: Calculates any of several measures of nestedness

nestedcontribution: Calculates the per-species contribution to nestedness...

nestedness: Calculates nestedness temperature of presence/absence...

nestedrank: Calculates the rank of a species in a matrix sorted for...

networklevel: Analysis of bipartite webs at the level of the entire network

nodespec: Calculates the node-based specialisation index

npartite: Computes indices for a masked-one-mode network

null.distr: Null model based on fitted marginal distribution

null.t.test: Compares observed pattern to random webs.

olesen2002aigrettes: A flower visitation network from the Azores

olesen2002flores: Another flower visitation network from the Azores

ollerton2003: ollerton2003

PDI: Paired Differences Index

plotModuleWeb: Function "plotModuleWeb"

plotPAC: Function to draw a circular plot to visualise potential...

plotweb: Visualize a bipartite interaction matrix (e.g. a foodweb)

printoutModuleInformation: Function printoutModuleInformation

projecting_tm: Projecting binary and weighted two-mode networks onto...

r2dexternal: Generates null models for network analysis by considering...

Safariland: A pollination web from Argentina

schemske1978: A flower visitation network from Urbana, IL, USA

second.extinct: Secondary extinctions in bipartite networks

shuffle.web: Shuffle web entries

slope.bipartite: Slope of extinction simulation

small1976: A flower visitation network from a peat bog in Ottawa, Canada

sortweb: Function to sort bipartite webs

specieslevel: Calculate various indices for network properties at the...

strength: Computes species strength according to either of two...

swap.web: Creates null model for bipartite networks

symmetrise_w: Symmetrise_w

tnet_igraph: Exports a tnet network to an igraph object

togetherness: Calculates the number of identical co-presences and...

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.

versionlog: Log of bipartite versions and changes

visweb: Plotting function to visualize a bipartite food web

V.ratio: Calculates the variance-ratio as suggested by Schluter (1984)

web2edges: Conversion of a network matrix into a (weighted) edge list

webs2array: Puts two or more webs into one array of webs

Files in this package

bipartite
bipartite/inst
bipartite/inst/CITATION
bipartite/inst/doc
bipartite/inst/doc/Dormann2011NetworkBiology.pdf
bipartite/inst/doc/Dormann2008Rnews.pdf
bipartite/inst/doc/Dormann2009OpenEcolJ.pdf
bipartite/src
bipartite/src/splittree.h
bipartite/src/bmn5.cc
bipartite/src/MersenneTwister.h
bipartite/src/identifyModules.cc
bipartite/src/graph.h
bipartite/src/rbtree.h
bipartite/src/dendro.h
bipartite/NAMESPACE
bipartite/data
bipartite/data/barrett1987.rda
bipartite/data/junker2013.rda
bipartite/data/memmott1999.rda
bipartite/data/schemske1978.rda
bipartite/data/olesen2002flores.rda
bipartite/data/vazllao.rda
bipartite/data/Safariland.rda
bipartite/data/olesen2002aigrettes.rda
bipartite/data/kevan1970.rda
bipartite/data/motten1982.rda
bipartite/data/kato1990.rda
bipartite/data/elberling1999.rda
bipartite/data/vazmasnc.rda
bipartite/data/vazarr.rda
bipartite/data/inouye1988.rda
bipartite/data/vazcer.rda
bipartite/data/mosquin1967.rda
bipartite/data/vazmasc.rda
bipartite/data/ollerton2003.rda
bipartite/data/vazquenc.rda
bipartite/data/vazquec.rda
bipartite/data/bezerra2009.rda
bipartite/data/small1976.rda
bipartite/R
bipartite/R/nestedness.r
bipartite/R/plotModuleWeb.R bipartite/R/plotPAC.R bipartite/R/shuffle.web.R bipartite/R/getModuleCoordinates.R bipartite/R/closeness_w.R bipartite/R/empty.R bipartite/R/grouplevel.R bipartite/R/strength.R bipartite/R/fc.R bipartite/R/degreedistr.R bipartite/R/clustering_tm.R
bipartite/R/PAC.r
bipartite/R/linklevel.R
bipartite/R/genweb.r
bipartite/R/nodespec.r
bipartite/R/C.score.R bipartite/R/npartite.R bipartite/R/networklevel.R
bipartite/R/nullmodel.r
bipartite/R/drawModules.R bipartite/R/projecting_tm.R bipartite/R/specieslevel.R
bipartite/R/null.t.test.r
bipartite/R/swap.web.R bipartite/R/as.tnet.R bipartite/R/plotweb.R bipartite/R/distance_w.R
bipartite/R/as.one.mode.r
bipartite/R/ND.r
bipartite/R/wine.r
bipartite/R/prepareWebForPlottingModules.R bipartite/R/second.extinct.R bipartite/R/plotweb2.R bipartite/R/V.ratio.R bipartite/R/H2fun.R bipartite/R/mgen.R bipartite/R/symmetrise_w.R bipartite/R/webs2array.R bipartite/R/visweb.R
bipartite/R/robustness.r
bipartite/R/dfun.R bipartite/R/endpoint.R bipartite/R/frame2webs.R bipartite/R/nestedcontribution.R bipartite/R/czvalues.R bipartite/R/extinction.R bipartite/R/web2edges.R bipartite/R/nestedrank.R
bipartite/R/nested.r
bipartite/R/compart.R
bipartite/R/discrepancy.r
bipartite/R/slope.bipartite.R bipartite/R/r2dexternal.R
bipartite/R/togetherness.r
bipartite/R/null.distr.r
bipartite/R/sortweb.r
bipartite/R/PDI.R bipartite/R/computeModules.R bipartite/R/zzz.R bipartite/R/tnet_igraph.R bipartite/R/versionlog.R bipartite/R/betweenness_w.R
bipartite/R/vaznull.r
bipartite/MD5
bipartite/DESCRIPTION
bipartite/man
bipartite/man/elberling1999.Rd bipartite/man/V.ratio.Rd
bipartite/man/robustness.rd
bipartite/man/visweb.Rd bipartite/man/as.tnet.Rd bipartite/man/plotweb.Rd bipartite/man/olesen2002flores.Rd bipartite/man/PDI.Rd bipartite/man/compart.Rd
bipartite/man/plotweb2.rd
bipartite/man/bezerra2009.Rd bipartite/man/nestedrank.Rd bipartite/man/npartite.Rd bipartite/man/second.extinct.Rd bipartite/man/moduleWeb-class.Rd bipartite/man/computeModules.Rd bipartite/man/junker2013.Rd bipartite/man/dfun.Rd
bipartite/man/nullmodel.rd
bipartite/man/motten1982.Rd bipartite/man/printoutModuleInformation.Rd bipartite/man/discrepancy.Rd bipartite/man/czvalues.Rd bipartite/man/closeness_w.Rd bipartite/man/plotModuleWeb.Rd bipartite/man/null.t.test.Rd bipartite/man/endpoint.Rd bipartite/man/clustering_tm.Rd bipartite/man/plotPAC.Rd bipartite/man/nodespec.Rd bipartite/man/fc.Rd bipartite/man/linklevel.Rd bipartite/man/vazmasc.Rd bipartite/man/shuffle.web.Rd bipartite/man/inouye1988.Rd bipartite/man/betweenness_w.Rd bipartite/man/nested.Rd bipartite/man/kato1990.Rd bipartite/man/bipartite-package.Rd bipartite/man/networklevel.Rd bipartite/man/genweb.Rd bipartite/man/C.score.Rd bipartite/man/empty.Rd
bipartite/man/wine.rd
bipartite/man/distance_w.Rd bipartite/man/projecting_tm.Rd bipartite/man/togetherness.Rd bipartite/man/vazquec.Rd bipartite/man/Safariland.Rd
bipartite/man/ND.rd
bipartite/man/r2dexternal.Rd bipartite/man/H2fun.Rd bipartite/man/vazmasnc.Rd bipartite/man/mosquin1967.Rd bipartite/man/vazcer.Rd bipartite/man/null.distr.Rd bipartite/man/tnet_igraph.Rd bipartite/man/kevan1970.Rd bipartite/man/slope.bipartite.Rd bipartite/man/webs2array.Rd bipartite/man/web2edges.Rd bipartite/man/grouplevel.Rd bipartite/man/as.one.mode.Rd bipartite/man/swap.web.Rd bipartite/man/versionlog.Rd bipartite/man/barrett1987.Rd
bipartite/man/PAC.rd
bipartite/man/olesen2002aigrettes.Rd bipartite/man/nestedness.Rd bipartite/man/memmott1999.Rd bipartite/man/degreedistr.Rd bipartite/man/specieslevel.Rd bipartite/man/frame2webs.Rd bipartite/man/sortweb.Rd bipartite/man/ollerton2003.Rd bipartite/man/symmetrise_w.Rd bipartite/man/listModuleInformation.Rd bipartite/man/schemske1978.Rd bipartite/man/vazarr.Rd bipartite/man/nestedcontribution.Rd bipartite/man/mgen.Rd bipartite/man/vazllao.Rd bipartite/man/small1976.Rd bipartite/man/vazquenc.Rd
bipartite/man/vazquez.example.rd
bipartite/man/vaznull.rd
bipartite/man/strength.Rd bipartite/man/extinction.Rd

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