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

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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.

Author
Carsten 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 publication
2016-11-08 11:49:49
Maintainer
Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
License
GPL
Version
2.07

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