bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices
Version 2.08

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.

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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 publication2017-03-31 06:30:25 UTC
MaintainerCarsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
LicenseGPL
Version2.08
URL https://github.com/biometry/bipartite
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bipartite")

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 clustering 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...
modulesLPA: Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"
moduleWeb-class: Class "moduleWeb"
mosquin1967: Flower visitation network from Melville Island, Northwest...
motten1982: A spring flower visitation network from North Carolina, USA
ND: Normalised degree, betweenness and closeness centrality
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
NOS: Calculates the node overlap and separation according to...
npartite: Computes indices for a masked-one-mode network
null.distr: Null model based on fitted marginal distribution
nullmodel: Generates null models for network analysis
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
PAC: Potential for Apparent Competition
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)
plotweb2: Visualize a tripartite interaction matrix (e.g. a tritrophic...
printoutModuleInformation: Function printoutModuleInformation
projecting_tm: Projecting binary and weighted two-mode networks onto...
r2dexternal: Generates null models for network analysis by considering...
robustness: Robustness to species extinctions
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.
vaznull: Null model with constrained connectance and moderately...
vazquec: A pollination network.
vazquenc: A pollination network.
vazquez.example: Examples for some analyses
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
wine: Weighted-Interaction Nestedness Estimator

Functions

.networklevel Man page
BC Man page Source code
BarbersMatrix Man page Source code
C.score Man page Source code
CC Man page Source code
DIRT_LPA_wb_plus Man page Source code
DIVISION Man page Source code
H2fun Man page
LOCALMAXIMISATION Man page Source code
LPA_wb_plus Man page Source code
ND Man page Source code
NOS Man page Source code
PAC Man page Source code
PDI Man page Source code
Safariland Man page
StageOne_LPAwbdash Man page Source code
StageTwo_LPAwbdash Man page Source code
TRACE Man page Source code
V.ratio Man page Source code
WEIGHTEDMODULARITY Man page Source code
WEIGHTEDMODULARITY2 Man page Source code
addEmptyColToMatrix Man page Source code
addEmptyRowToMatrix Man page Source code
as.one.mode Man page Source code
as.tnet Man page
barrett1987 Man page
betweenness_w Man page
bezerra2009 Man page
bipartite Man page
bipartite-package Man page
cM Man page Source code
closeness_w Man page
clustering_tm Man page
compart Man page Source code
computeModules Man page Source code
confint Man page
convert2moduleWeb Man page Source code
czvalues Man page Source code
degreedistr Man page
deleteModuleData Man page Source code
dfun Man page Source code
discrepancy Man page Source code
distance_w Man page
drawModules Man page Source code
elberling1999 Man page
empty Man page
endpoint Man page Source code
extinction Man page Source code
fc Man page Source code
fd Man page
frame2webs Man page Source code
genweb Man page
getModuleCoordinates Man page Source code
grouplevel Man page Source code
inouye1988 Man page
intasymm Man page
intereven Man page
isCorrectModuleWebObject Man page Source code Source code
junker2013 Man page
kato1990 Man page
kevan1970 Man page
linklevel Man page Source code
listModuleInformation Man page Source code
memmott1999 Man page
metaComputeModules Man page Source code
mgen Man page Source code
mlik Man page
moduleWeb-class Man page
mosquin1967 Man page
motten1982 Man page
nested Man page Source code
nestedcontribution Man page Source code
nestedness Man page Source code
nestedrank Man page Source code
netstats Man page
networklevel Man page Source code
nodespec Man page Source code
npartite Man page Source code
null.distr Man page Source code
null.t.test Man page Source code
nullmodel Man page Source code
olesen2002aigrettes Man page
olesen2002flores Man page
ollerton2003 Man page
onAttach Source code
onLoad Source code
one.grouplevel Man page Source code
plot.wine Man page Source code
plotModuleWeb Man page Source code
plotPAC Man page Source code
plotmat Man page
plotweb Man page
plotweb2 Man page
prepareWebForPlottingModules Man page Source code
printoutModuleInformation Man page Source code
projecting_tm Man page
quant2bin Man page
r2dexternal Man page Source code
readModuleData Man page Source code
robustness Man page Source code
schemske1978 Man page
second.extinct Man page
shuffle.web Man page
slope.bipartite Man page
small1976 Man page
sortmatr Man page
sortmatrext Man page
sortweb Man page Source code
specieslevel Man page Source code
strength Man page Source code
swap.web Man page Source code
symmetrise_w Man page
tnet_igraph Man page
togetherness Man page Source code
vazarr Man page
vazcer Man page
vazllao Man page
vazmasc Man page
vazmasnc Man page
vaznull Man page Source code
vazquec Man page
vazquenc Man page
vazquez.example Man page
versionlog Man page Man page Source code
visweb Man page Source code
web2edges Man page Source code
webs2array Man page Source code
wine Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Dormann2011NetworkBiology.pdf
inst/doc/Dormann2008Rnews.pdf
inst/doc/Dormann2009OpenEcolJ.pdf
src
src/splittree.h
src/bmn5.cc
src/MersenneTwister.h
src/identifyModules.cc
src/graph.h
src/rbtree.h
src/init.c
src/dendro.h
NAMESPACE
data
data/barrett1987.rda
data/junker2013.rda
data/memmott1999.rda
data/schemske1978.rda
data/olesen2002flores.rda
data/vazllao.rda
data/Safariland.rda
data/olesen2002aigrettes.rda
data/kevan1970.rda
data/motten1982.rda
data/kato1990.rda
data/elberling1999.rda
data/vazmasnc.rda
data/vazarr.rda
data/inouye1988.rda
data/vazcer.rda
data/mosquin1967.rda
data/vazmasc.rda
data/ollerton2003.rda
data/vazquenc.rda
data/vazquec.rda
data/bezerra2009.rda
data/small1976.rda
R
R/nestedness.r
R/plotModuleWeb.R
R/plotPAC.R
R/shuffle.web.R
R/getModuleCoordinates.R
R/closeness_w.R
R/empty.R
R/grouplevel.R
R/strength.R
R/fc.R
R/NOS.R
R/degreedistr.R
R/clustering_tm.R
R/PAC.r
R/linklevel.R
R/genweb.r
R/nodespec.r
R/C.score.R
R/npartite.R
R/networklevel.R
R/nullmodel.r
R/drawModules.R
R/projecting_tm.R
R/specieslevel.R
R/null.t.test.r
R/swap.web.R
R/as.tnet.R
R/plotweb.R
R/distance_w.R
R/as.one.mode.r
R/modulesLPA.R
R/ND.r
R/wine.r
R/prepareWebForPlottingModules.R
R/second.extinct.R
R/plotweb2.R
R/V.ratio.R
R/H2fun.R
R/mgen.R
R/symmetrise_w.R
R/webs2array.R
R/visweb.R
R/robustness.r
R/dfun.R
R/endpoint.R
R/frame2webs.R
R/nestedcontribution.R
R/czvalues.R
R/extinction.R
R/web2edges.R
R/nestedrank.R
R/nested.r
R/compart.R
R/discrepancy.r
R/slope.bipartite.R
R/r2dexternal.R
R/togetherness.r
R/metaComputeModules.R
R/null.distr.r
R/sortweb.r
R/PDI.R
R/computeModules.R
R/zzz.R
R/tnet_igraph.R
R/versionlog.R
R/betweenness_w.R
R/vaznull.r
MD5
DESCRIPTION
man
man/elberling1999.Rd
man/V.ratio.Rd
man/robustness.rd
man/visweb.Rd
man/as.tnet.Rd
man/plotweb.Rd
man/olesen2002flores.Rd
man/PDI.Rd
man/compart.Rd
man/plotweb2.rd
man/bezerra2009.Rd
man/nestedrank.Rd
man/npartite.Rd
man/second.extinct.Rd
man/moduleWeb-class.Rd
man/computeModules.Rd
man/junker2013.Rd
man/dfun.Rd
man/nullmodel.rd
man/motten1982.Rd
man/printoutModuleInformation.Rd
man/discrepancy.Rd
man/czvalues.Rd
man/closeness_w.Rd
man/plotModuleWeb.Rd
man/null.t.test.Rd
man/endpoint.Rd
man/clustering_tm.Rd
man/plotPAC.Rd
man/nodespec.Rd
man/fc.Rd
man/linklevel.Rd
man/vazmasc.Rd
man/shuffle.web.Rd
man/inouye1988.Rd
man/betweenness_w.Rd
man/nested.Rd
man/kato1990.Rd
man/bipartite-package.Rd
man/networklevel.Rd
man/genweb.Rd
man/C.score.Rd
man/empty.Rd
man/wine.rd
man/distance_w.Rd
man/projecting_tm.Rd
man/togetherness.Rd
man/vazquec.Rd
man/Safariland.Rd
man/ND.rd
man/r2dexternal.Rd
man/H2fun.Rd
man/vazmasnc.Rd
man/mosquin1967.Rd
man/vazcer.Rd
man/null.distr.Rd
man/tnet_igraph.Rd
man/kevan1970.Rd
man/slope.bipartite.Rd
man/webs2array.Rd
man/web2edges.Rd
man/grouplevel.Rd
man/as.one.mode.Rd
man/swap.web.Rd
man/versionlog.Rd
man/barrett1987.Rd
man/PAC.rd
man/olesen2002aigrettes.Rd
man/nestedness.Rd
man/memmott1999.Rd
man/degreedistr.Rd
man/specieslevel.Rd
man/frame2webs.Rd
man/sortweb.Rd
man/ollerton2003.Rd
man/symmetrise_w.Rd
man/NOS.Rd
man/listModuleInformation.Rd
man/schemske1978.Rd
man/vazarr.Rd
man/nestedcontribution.Rd
man/mgen.Rd
man/vazllao.Rd
man/small1976.Rd
man/modulesLPA.Rd
man/vazquenc.Rd
man/vazquez.example.rd
man/vaznull.rd
man/strength.Rd
man/extinction.Rd
bipartite documentation built on May 19, 2017, 11:36 p.m.