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

Functions

addEmptyColToMatrix Man page
addEmptyRowToMatrix Man page
as.one.mode Man page
as.tnet Man page
barrett1987 Man page
betweenness_w Man page
bezerra2009 Man page
bipartite Man page
bipartite-package Man page
closeness_w Man page
clustering_tm Man page
cM Man page
compart Man page
computeModules Man page
C.score Man page
czvalues Man page
degreedistr Man page
deleteModuleData Man page
dfun Man page
discrepancy Man page
distance_w Man page
drawModules Man page
elberling1999 Man page
empty Man page
endpoint Man page
extinction Man page
fc Man page
fd Man page
frame2webs Man page
genweb Man page
getModuleCoordinates Man page
grouplevel Man page
H2fun Man page
inouye1988 Man page
isCorrectModuleWebObject Man page
junker2013 Man page
kato1990 Man page
kevan1970 Man page
linklevel Man page
listModuleInformation Man page
memmott1999 Man page
mgen Man page
moduleWeb-class Man page
mosquin1967 Man page
motten1982 Man page
nested Man page
nestedcontribution Man page
nestedness Man page
nestedrank Man page
networklevel Man page
.networklevel Man page
nodespec Man page
npartite Man page
null.distr Man page
null.t.test Man page
olesen2002aigrettes Man page
olesen2002flores Man page
ollerton2003 Man page
one.grouplevel Man page
PDI Man page
plotModuleWeb Man page
plotPAC Man page
plotweb Man page
prepareWebForPlottingModules Man page
printoutModuleInformation Man page
projecting_tm Man page
r2dexternal Man page
readModuleData Man page
Safariland Man page
schemske1978 Man page
second.extinct Man page
shuffle.web Man page
slope.bipartite Man page
small1976 Man page
sortweb Man page
specieslevel Man page
strength Man page
swap.web Man page
symmetrise_w Man page
tnet_igraph Man page
togetherness Man page
vazarr Man page
vazcer Man page
vazllao Man page
vazmasc Man page
vazmasnc Man page
vazquec Man page
vazquenc Man page
versionlog Man page
versionlog Man page
visweb Man page
V.ratio Man page
web2edges Man page
webs2array Man page

Files

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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