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bipartite (version 2.23)

Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Description

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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Install

install.packages('bipartite')

Monthly Downloads

13,137

Version

2.23

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

October 7th, 2025

Functions in bipartite (2.23)

Ensures that networks conform to the tnet stardards

Individuals caught in a pollination web in boreal Canada.

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

Calculate network dissimilarity (beta diversity) and its components

Betweenness centrality in a weighted network

Distance in a weighted network

Closeness centrality in a weighted network

Redefined clustering coefficient for two-mode networks

Calculates discrepancy of a matrix

Indices of a bipartite network at the link level

Flower visitation network

Computes c and z for network modules

decimalr2dtable

Generates matrix with same marginal totals for non-negative decimal values

Deletes empty rows and columns from a matrix.

Simulates extinction of a species from a bipartite network

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

Detects compartments

listModuleInformation

listModuleInformation

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

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

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

Computes end-point degrees for a bipartite network

Generate a random bipartite web

A pollination network from Northern Ellesmere Island, Canada

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

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

Calculates the node-based specialisation index

moduleWeb-class

Class "moduleWeb"

nestedcontribution

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

Calculates nestedness temperature of presence/absence matrices

Plot a matrix organised by topology

Compares observed pattern to random webs.

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

Null model based on fitted marginal distribution

plotweb_deprecated

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

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

Calculates any of several measures of nestedness

printoutModuleInformation

printoutModuleInformation

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

olesen2002aigrettes

A flower visitation network from the Azores

Generates null models for network analysis

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

A flower visitation network from Urbana, IL, USA

Secondary extinctions in bipartite networks

Visualize a tripartite interaction matrix (e.g. a tritrophic foodweb)

Exports a tnet network to an igraph object

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

A pollination network.

Organise matrix by topology

Computes indices for a masked-one-mode network

Creates null model for bipartite networks

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

Generates null models for network analysis by considering external abundances

Shuffle web entries

Calculates the functional complementarity for the rows of a web

A pollination network.

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

slope.bipartite

Slope of extinction simulation

bipartite-package

Analysis of bipartite ecological webs

A pollination network.

A spring flower visitation network from North Carolina, USA

vazquez.example

Examples for some analyses

Log of bipartite versions and changes

Flower visitation network from Melville Island, Northwest Territories, Canada

A pollination network.

Generate simulated network according to a given probability matrix

Converts a table of observations into a network matrix

Flower visitation network from a meadow near Bristol, UK

The restricted null model accounting for modules with nested entries

olesen2002flores

Another flower visitation network from the Azores

Analysis of bipartite webs at the level of the entire network

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

Robustness to species extinctions

Computes species strength according to either of two definitions

spectral.radius

Calculates the spectral radius as a nestedness measurement of a bipartite matrix, possibly with regard to mass action

Plotting function to visualize a bipartite food web

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

Puts two or more webs into one array of webs

Weighted-Interaction Nestedness Estimator

A pollination network.

A pollination network.

A pollination network.

Null model with constrained connectance and moderately constrained marginal totals

A pollination network from the Canadian Rockies

Function to sort bipartite webs

Calculate various indices for network properties at the species level

A pollination web from Argentina

Paired Differences Index

Calculates the node overlap and separation according to Strona & Veech (2015)

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

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

Normalised degree, betweenness and closeness centrality

Conversion of a network matrix

Specialisation of a bipartite web.

Reshape a webarray to a web X link matrix

Potential for Apparent Competition