# Visualising bipartite networks and calculating some (ecological) indices.

## Documentation for package ‘bipartite’ version 1.17

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

bipartite-package | Analysis of bipartite ecological webs.
addEmptyColToMatrix | Function "plotModuleWeb"
addEmptyRowToMatrix | Function "plotModuleWeb"
as.one.mode | Conversion of a network matrix
barrett1987 | Individuals caught in a pollination web in boreal Canada.
BC | Normalised degree, betweenness and closeness centrality
bezerra2009 | Individuals observed in a flower-visitation networks of oil-collecting bees in a Brazilian steppe.
bipartite | Analysis of bipartite ecological webs.
C.score | Calculates the (normalised) mean number of checkerboard combinations (C-score) in a matrix
CC | Normalised degree, betweenness and closeness centrality
cM | Function "computeModules"
compart | Detects compartments
computeModules | Function "computeModules"
confint | Examples for some analyses
degreedistr | Fits functions to cumulative degree distributions of both trophic levels of a network.
deleteModuleData | Function "computeModules"
dfun | Calculates standardised specialisation index d' (d prime) for each species in the lower trophic level of a bipartite network.
discrepancy | Calculates discrepancy of a matrix
drawModules | Function "plotModuleWeb"
elberling1999 | No. of visits in a pollination web of arctic-alpine Sweden
empty | Deletes empty rows and columns from a matrix.
extinction | Simulates extinction of a species from a bipartite network
genweb | Generate a random bipartite web
getModuleCoordinates | Function "plotModuleWeb"
H2fun | Specialisation of a bipartite web.
inouye1988 | A pollination network from the Snowy Mountains of New South Wales, Australia
intasymm | Examples for some analyses
intereven | Examples for some analyses
isCorrectModuleWebObject | Function "plotModuleWeb"
kato1990 | No. of individuals caught in a pollination web of a Japanese beech forest
kevan1970 | A pollination network from Northern Ellesmere Island, Canada
listModuleInformation | Function "listModuleInformation"
memmott1999 | Flower visitation network from a meadow near Bristol, UK
mgen | Examples for some analyses
mlik | Examples for some analyses
moduleWeb-class | Class "moduleWeb"
mosquin1967 | Flower visitation network from Melville Island, Northwest Territories, Canada
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
nestedness | Calculates nestedness temperature of presence/absence matrices
netstats | Examples for some analyses
networklevel | Analysis of bipartite webs at the level of the entire network
nodespec | Calculates the node-based specialisation index
null.distr | Null model based on fitted marginal distribution
null.t.test | Compares observed pattern to random webs.
nullmodel | Generates null models for network analysis
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
plot.wine | Weighted-Interaction Nestedness Estimator
plotmat | Examples for some analyses
plotModuleWeb | Function "plotModuleWeb"
plotPAC | Function to draw a circular plot to visualise potential apparent competition (PAC)
plotweb | Visualize a bipartite interaction matrix (e.g. a foodweb)
plotweb2 | Visualize a tripartite interaction matrix (e.g. a tritrophic foodweb)
prepareWebForPlottingModules | Function "plotModuleWeb"
printoutModuleInformation | Function printoutModuleInformation
quant2bin | Examples for some analyses
readModuleData | Function "computeModules"
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
sortmatr | Examples for some analyses
sortmatrext | Examples for some analyses
sortweb | Function to sort bipartite webs
specieslevel | Calculate various indices for network properties at the species level
swap.web | Creates null model for bipartite networks
togetherness | Calculates the number of identical co-presences and co-absences for species-on-islands
V.ratio | Calculates the variance-ratio as suggested by Schluter (1984)
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 totals and connectance
vazquec | A pollination network.
vazquenc | A pollination network.
vazquez.example | Examples for some analyses
visweb | Plotting function to visualize a bipartite food web
web2edges | Conversion of a network matrix into a (weighted) edge list
wine | Weighted-Interaction Nestedness Estimator