# Visualising Bipartite Networks and Calculating Some (Ecological) Indices

## Documentation for package ‘bipartite’ version 2.20

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T V W

bipartite-package | Analysis of bipartite ecological webs

## -- A --

addEmptyColToMatrix | plotModuleWeb
addEmptyRowToMatrix | plotModuleWeb
array2linkmx | Reshape a webarray to a web X link matrix
as.one.mode | Conversion of a network matrix
as.tnet | Ensures that networks conform to the tnet stardards

## -- B --

barrett1987 | Individuals caught in a pollination web in boreal Canada.
BC | Normalised degree, betweenness and closeness centrality
betalinkr | Calculate network dissimilarity (beta diversity) and its components
betalinkr_multi | Calculate network dissimilarity (beta diversity) and its components
betweenness_w | Betweenness centrality in a weighted network
bezerra2009 | Individuals observed in a flower-visitation network of oil-collecting bees in a Brazilian steppe.
bipartite | Analysis of bipartite ecological webs

## -- C --

C.score | Calculates the (normalised) mean number of checkerboard combinations (C-score) in a matrix
CC | Normalised degree, betweenness and closeness centrality
closeness_w | Closeness centrality in a weighted network
clustering_tm | Redefined clustering coefficient for two-mode networks
compart | Detects compartments
computeModules | computeModules
confint | Examples for some analyses
convert2moduleWeb | Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"
czvalues | Computes c and z for network modules

## -- D --

decimalr2dtable | Generates matrix with same marginal totals for non-negative decimal values
degreedistr | Fits functions to cumulative degree distributions of both trophic levels of a network.
dfun | Calculates standardised specialisation index d' (d prime) for each species in the lower trophic level of a bipartite network.
DIRT_LPA_wb_plus | Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"
discrepancy | Calculates discrepancy of a matrix
distance_w | Distance in a weighted network
drawModules | plotModuleWeb

## -- E --

edgelist2webs | Converts a table of observations into a network matrix
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

## -- F --

fc | Calculates the functional complementarity for the rows of a web
fd | Calculates the functional complementarity for the rows of a web
frame2webs | Converts a table of observations into a network matrix

## -- G --

genweb | Generate a random bipartite web
getModuleCoordinates | plotModuleWeb
grouplevel | Analysis of bipartite webs at the level of each of the two levels (groups) of the network

## -- H --

H2fun | Specialisation of a bipartite web.

## -- I --

inouye1988 | A pollination network from the Snowy Mountains of New South Wales, Australia
intasymm | Examples for some analyses
intereven | Examples for some analyses
isCorrectModuleWebObject | plotModuleWeb

## -- J --

junker2013 | Flower visitation network

## -- K --

kato1990 | No. of individuals caught in a pollination web of a Japanese beech forest
kevan1970 | A pollination network from Northern Ellesmere Island, Canada

## -- L --

linklevel | Indices of a bipartite network at the link level
listModuleInformation | listModuleInformation
LPA_wb_plus | Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

## -- M --

memmott1999 | Flower visitation network from a meadow near Bristol, UK
metaComputeModules | computeModules
mgen | Generate simulated network according to a given probability matrix
mlik | Examples for some analyses
module2constraints | Computes nestedness of a matrix as WNODA (and NODF and WNODF)
moduleWeb-class | Class "moduleWeb"
mosquin1967 | Flower visitation network from Melville Island, Northwest Territories, Canada
motten1982 | A spring flower visitation network from North Carolina, USA

## -- N --

ND | Normalised degree, betweenness and closeness centrality
nest.smdm | Computes nestedness of a matrix as WNODA (and NODF and WNODF)
nested | Calculates any of several measures of nestedness
nestedcontribution | Calculates the per-species contribution to nestedness (z-score relative to null model)
nestedness | Calculates nestedness temperature of presence/absence matrices
nestedrank | Calculates the rank of a species in a matrix sorted for maximum nestedness
netstats | Examples for some analyses
networklevel | Analysis of bipartite webs at the level of the entire network
nodespec | Calculates the node-based specialisation index
NODF | Computes nestedness of a matrix as WNODA (and NODF and WNODF)
NOS | Calculates the node overlap and separation according to Strona & Veech (2015)
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.
nullmodel | Generates null models for network analysis

## -- O --

olesen2002aigrettes | A flower visitation network from the Azores
olesen2002flores | Another flower visitation network from the Azores
olito2015 | A pollination network from the Canadian Rockies
ollerton2003 | ollerton2003
one.grouplevel | Analysis of bipartite webs at the level of each of the two levels (groups) of the network

## -- P --

PAC | Potential for Apparent Competition
PDI | Paired Differences Index
plot.wine | Weighted-Interaction Nestedness Estimator
plotmat | Examples for some analyses
plotmatrix | Plot a matrix organised by topology
plotModuleWeb | 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)
PosteriorProb | The restricted null model accounting for modules with nested entries
prepareWebForPlottingModules | plotModuleWeb
printoutModuleInformation | printoutModuleInformation
projecting_tm | Projecting binary and weighted two-mode networks onto weighted one-mode networks.

## -- Q --

quant2bin | Examples for some analyses

## -- R --

r2dexternal | Generates null models for network analysis by considering external abundances
readModuleData | computeModules
restrictednull | The restricted null model accounting for modules with nested entries
robustness | Robustness to species extinctions

## -- S --

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
sortmatrix | Organise matrix by topology
sortweb | Function to sort bipartite webs
specieslevel | Calculate various indices for network properties at the species level
strength | Computes species strength according to either of two definitions
swap.web | Creates null model for bipartite networks
symmetrise_w | Symmetrise_w

## -- T --

tnet_igraph | Exports a tnet network to an igraph object
togetherness | Calculates the number of identical co-presences and co-absences for species-on-islands

## -- V --

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 connectance and moderately constrained marginal totals
vaznullexternal | Generates null models for network analysis by considering external abundances
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

## -- W --

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
WNODA | Computes nestedness of a matrix as WNODA (and NODF and WNODF)
WNODF | Computes nestedness of a matrix as WNODA (and NODF and WNODF)