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bipartite (version 2.21)

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.packages('bipartite')

Monthly Downloads

4,933

Version

2.21

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

February 20th, 2025

Functions in bipartite (2.21)

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

Ensures that networks conform to the tnet stardards

Betweenness centrality in a weighted network

Calculate network dissimilarity (beta diversity) and its components

Closeness centrality in a weighted network

Individuals caught in a pollination web in boreal Canada.

Detects compartments

bipartite-package

Analysis of bipartite ecological webs

Redefined clustering coefficient for two-mode networks

Distance in a weighted network

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

Calculates discrepancy of a matrix

Deletes empty rows and columns from a matrix.

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

Simulates extinction of a species from a bipartite network

Computes end-point degrees for a bipartite network

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

Computes c and z for network modules

Calculates the functional complementarity for the rows of a web

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

Generate a random bipartite web

decimalr2dtable

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

Converts a table of observations into a network matrix

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

A pollination network from Northern Ellesmere Island, Canada

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

moduleWeb-class

Class "moduleWeb"

Indices of a bipartite network at the link level

Calculates any of several measures of nestedness

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

Generate simulated network according to a given probability matrix

listModuleInformation

listModuleInformation

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

Compares observed pattern to random webs.

Null model based on fitted marginal distribution

nestedcontribution

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

Flower visitation network from a meadow near Bristol, UK

A spring flower visitation network from North Carolina, USA

Flower visitation network from Melville Island, Northwest Territories, Canada

Flower visitation network

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

Analysis of bipartite webs at the level of the entire network

Generates null models for network analysis by considering external abundances

Calculates the node-based specialisation index

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

Calculates nestedness temperature of presence/absence matrices

Robustness to species extinctions

Computes indices for a masked-one-mode network

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

spectral.radius

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

Secondary extinctions in bipartite networks

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

Calculate various indices for network properties at the species level

printoutModuleInformation

printoutModuleInformation

A flower visitation network from Urbana, IL, USA

Shuffle web entries

Generates null models for network analysis

Exports a tnet network to an igraph object

The restricted null model accounting for modules with nested entries

A pollination network.

olesen2002aigrettes

A flower visitation network from the Azores

A pollination network.

Organise matrix by topology

olesen2002flores

Another flower visitation network from the Azores

Null model with constrained connectance and moderately constrained marginal totals

Plotting function to visualize a bipartite food web

Log of bipartite versions and changes

Plot a matrix organised by topology

Creates null model for bipartite networks

Computes species strength according to either of two definitions

vazquez.example

Examples for some analyses

Function to sort bipartite webs

A pollination network.

slope.bipartite

Slope of extinction simulation

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

A pollination network.

A pollination network.

A pollination network from the Canadian Rockies

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

A pollination network.

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

Puts two or more webs into one array of webs

Weighted-Interaction Nestedness Estimator

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

A pollination network.

Paired Differences Index

Potential for Apparent Competition

Normalised degree, betweenness and closeness centrality

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

A pollination web from Argentina

Reshape a webarray to a web X link matrix

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

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

Specialisation of a bipartite web.

Conversion of a network matrix