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bipartite (version 2.18)

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

4,471

Version

2.18

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

October 18th, 2022

Functions in bipartite (2.18)

Reshape a webarray to a web X link matrix

Conversion of a network matrix

Specialisation of a bipartite web.

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

Calculate network dissimilarity (beta diversity) and its components

Betweenness centrality in a weighted network

Closeness centrality in a weighted network

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

Redefined clustering coefficient for two-mode networks

decimalr2dtable

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

Computes c and z for network modules

Ensures that networks conform to the tnet stardards

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

Individuals caught in a pollination web in boreal Canada.

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

Detects compartments

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

bipartite-package

Analysis of bipartite ecological webs

Distance in a weighted network

Calculates discrepancy of a matrix

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

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

Flower visitation network

A pollination network from Northern Ellesmere Island, Canada

Indices of a bipartite network at the link level

nestedcontribution

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

Deletes empty rows and columns from a matrix.

Calculates nestedness temperature of presence/absence matrices

listModuleInformation

listModuleInformation

Generate simulated network according to a given probability matrix

Simulates extinction of a species from a bipartite network

Generate a random bipartite web

Computes end-point degrees for a bipartite network

Flower visitation network from a meadow near Bristol, UK

Converts a table of observations into a network matrix

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

Calculates any of several measures of nestedness

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

Calculates the functional complementarity for the rows of a web

Computes indices for a masked-one-mode network

A spring flower visitation network from North Carolina, USA

Calculates the node-based specialisation index

Flower visitation network from Melville Island, Northwest Territories, Canada

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

moduleWeb-class

Class "moduleWeb"

Analysis of bipartite webs at the level of the entire network

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

olesen2002flores

Another flower visitation network from the Azores

olesen2002aigrettes

A flower visitation network from the Azores

Null model based on fitted marginal distribution

Generates null models for network analysis

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

Compares observed pattern to random webs.

printoutModuleInformation

printoutModuleInformation

Plot a matrix organised by topology

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

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

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

Generates null models for network analysis by considering external abundances

The restricted null model accounting for modules with nested entries

A pollination network from the Canadian Rockies

Calculate various indices for network properties at the species level

Organise matrix by topology

A flower visitation network from Urbana, IL, USA

Function to sort bipartite webs

Robustness to species extinctions

Shuffle web entries

Computes species strength according to either of two definitions

A pollination network.

Secondary extinctions in bipartite networks

A pollination network.

A pollination network.

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

slope.bipartite

Slope of extinction simulation

Creates null model for bipartite networks

A pollination network.

Exports a tnet network to an igraph object

A pollination network.

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

Null model with constrained connectance and moderately constrained marginal totals

A pollination network.

Puts two or more webs into one array of webs

A pollination network.

Weighted-Interaction Nestedness Estimator

vazquez.example

Examples for some analyses

Log of bipartite versions and changes

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

Plotting function to visualize a bipartite food web

Normalised degree, betweenness and closeness centrality

Potential for Apparent Competition

Paired Differences Index

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

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

A pollination web from Argentina