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bipartite (version 2.19)

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

4,452

Version

2.19

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

November 30th, 2023

Functions in bipartite (2.19)

Individuals caught in a pollination web in boreal Canada.

Redefined clustering coefficient for two-mode networks

Ensures that networks conform to the tnet stardards

Detects compartments

Closeness centrality in a weighted network

Calculate network dissimilarity (beta diversity) and its components

Betweenness centrality in a weighted network

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

bipartite-package

Analysis of bipartite ecological webs

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

Distance in a weighted network

Simulates extinction of a species from a bipartite network

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

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

Computes c and z for network modules

Computes end-point degrees for a bipartite network

Deletes empty rows and columns from a matrix.

Calculates discrepancy of a matrix

decimalr2dtable

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

listModuleInformation

listModuleInformation

Flower visitation network

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

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

Indices of a bipartite network at the link level

Calculates the functional complementarity for the rows of a web

Generate a random bipartite web

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

A pollination network from Northern Ellesmere Island, Canada

Converts a table of observations into a network matrix

moduleWeb-class

Class "moduleWeb"

nestedcontribution

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

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

Flower visitation network from a meadow near Bristol, UK

A spring flower visitation network from North Carolina, USA

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

Flower visitation network from Melville Island, Northwest Territories, Canada

Generate simulated network according to a given probability matrix

Calculates nestedness temperature of presence/absence matrices

Calculates any of several measures of nestedness

Null model based on fitted marginal distribution

Generates null models for network analysis

olesen2002flores

Another flower visitation network from the Azores

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

Compares observed pattern to random webs.

Calculates the node-based specialisation index

Computes indices for a masked-one-mode network

A pollination network from the Canadian Rockies

Analysis of bipartite webs at the level of the entire network

olesen2002aigrettes

A flower visitation network from the Azores

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

Generates null models for network analysis by considering external abundances

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

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

Plot a matrix organised by topology

The restricted null model accounting for modules with nested entries

printoutModuleInformation

printoutModuleInformation

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

slope.bipartite

Slope of extinction simulation

Organise matrix by topology

Calculate various indices for network properties at the species level

Computes species strength according to either of two definitions

Robustness to species extinctions

A flower visitation network from Urbana, IL, USA

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

Shuffle web entries

Secondary extinctions in bipartite networks

Exports a tnet network to an igraph object

Function to sort bipartite webs

A pollination network.

A pollination network.

A pollination network.

Creates null model for bipartite networks

A pollination network.

A pollination network.

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

A pollination network.

Null model with constrained connectance and moderately constrained marginal totals

A pollination network.

Puts two or more webs into one array of webs

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

Plotting function to visualize a bipartite food web

Weighted-Interaction Nestedness Estimator

Log of bipartite versions and changes

vazquez.example

Examples for some analyses

A pollination web from Argentina

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

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

Normalised degree, betweenness and closeness centrality

Reshape a webarray to a web X link matrix

Specialisation of a bipartite web.

Conversion of a network matrix

Paired Differences Index

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

Potential for Apparent Competition