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bipartite (version 2.05)

Visualising bipartite networks and calculating some (ecological) indices.

Description

Bipartite provides 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 trophic levels, 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 webs topology.

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Version

Install

install.packages('bipartite')

Monthly Downloads

4,243

Version

2.05

License

GPL

Maintainer

Carsten F Dormann

Last Published

November 25th, 2014

Functions in bipartite (2.05)

elberling1999

No. of visits in a pollination web of arctic-alpine Sweden
V.ratio

Calculates the variance-ratio as suggested by Schluter (1984)
moduleWeb-class

Class "moduleWeb"
endpoint

Computes end-point degrees for a bipartite network
C.score

Calculates the (normalised) mean number of checkerboard combinations (C-score) in a matrix
bezerra2009

Individuals observed in a flower-visitation network of oil-collecting bees in a Brazilian steppe.
PDI

Paired Differences Index
distance_w

Distance in a weighted network
projecting_tm

Projecting binary and weighted two-mode networks onto weighted one-mode networks.
clustering_tm

Redefined clusering coefficient for two-mode networks
mgen

Generate simulated network according to a given probability matrix
schemske1978

A flower visitation network from Urbana, IL, USA
symmetrise_w

Symmetrise_w
junker2013

Flower visitation network
genweb

Generate a random bipartite web
webs2array

Puts two or more webs into one array of webs
shuffle.web

Shuffle web entries
motten1982

A spring flower visitation network from North Carolina, USA
second.extinct

Secondary extinctions in bipartite networks
discrepancy

Calculates discrepancy of a matrix
r2dexternal

Generates null models for network analysis by considering external abundances
listModuleInformation

Function "listModuleInformation"
npartite

Computes indices for a masked-one-mode network
kato1990

No. of individuals caught in a pollination web of a Japanese beech forest
compart

Detects compartments
nestedrank

Calculates the rank of a species in a matrix sorted for maximum nestedness
extinction

Simulates extinction of a species from a bipartite network
swap.web

Creates null model for bipartite networks
togetherness

Calculates the number of identical co-presences and co-absences for species-on-islands
vazquec

A pollination network.
sortweb

Function to sort bipartite webs
olesen2002aigrettes

A flower visitation network from the Azores
plotPAC

Function to draw a circular plot to visualise potential apparent competition (PAC)
closeness_w

Closeness centrality in a weighted network
null.t.test

Compares observed pattern to random webs.
null.distr

Null model based on fitted marginal distribution
nested

Calculates any of several measures of nestedness
kevan1970

A pollination network from Northern Ellesmere Island, Canada
nestedcontribution

Calculates the per-species contribution to nestedness (z-score relative to null model)
Safariland

A pollination web from Argentina
as.tnet

Ensures that networks conform to the tnet stardards
degreedistr

Fits functions to cumulative degree distributions of both trophic levels of a network.
grouplevel

Analysis of bipartite webs at the level of each of the two levels (groups) of the network
barrett1987

Individuals caught in a pollination web in boreal Canada.
dfun

Calculates standardised specialisation index d' (d prime) for each species in the lower trophic level of a bipartite network.
visweb

Plotting function to visualize a bipartite food web
betweenness_w

Betweenness centrality in a weighted network
bipartite-package

Analysis of bipartite ecological webs
olesen2002flores

Another flower visitation network from the Azores
slope.bipartite

Slope of extinction simulation
frame2webs

Converts a table of observations into a network matrix
mosquin1967

Flower visitation network from Melville Island, Northwest Territories, Canada
linklevel

Indices of a bipartite network at the link level
vazllao

A pollination network.
as.one.mode

Conversion of a network matrix
vazmasnc

A pollination network.
vazcer

A pollination network.
networklevel

Analysis of bipartite webs at the level of the entire network
czvalues

Computes c and z for network modules
fc

Calculates the functional complementarity for the rows of a web
versionlog

Log of bipartite versions and changes
vazarr

A pollination network.
nodespec

Calculates the node-based specialisation index
computeModules

Function "computeModules"
plotModuleWeb

Function "plotModuleWeb"
specieslevel

Calculate various indices for network properties at the species level
printoutModuleInformation

Function printoutModuleInformation
vazquenc

A pollination network.
tnet_igraph

Exports a tnet network to an igraph object
ollerton2003

ollerton2003
inouye1988

A pollination network from the Snowy Mountains of New South Wales, Australia
nestedness

Calculates nestedness temperature of presence/absence matrices
plotweb

Visualize a bipartite interaction matrix (e.g. a foodweb)
small1976

A flower visitation network from a peat bog in Ottawa, Canada
empty

Deletes empty rows and columns from a matrix.
memmott1999

Flower visitation network from a meadow near Bristol, UK
strength

Computes species strength according to either of two definitions
vazmasc

A pollination network.
H2fun

Specialisation of a bipartite web.
web2edges

Conversion of a network matrix into a (weighted) edge list