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bipartite (version 2.15)

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

4,957

Version

2.15

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

April 3rd, 2020

Functions in bipartite (2.15)

Reshape a webarray to a web X link matrix

Betweenness centrality in a weighted network

Ensures that networks conform to the tnet stardards

Paired Differences Index

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

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

Individuals caught in a pollination web in boreal Canada.

Generate simulated network according to a given probability matrix

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

Specialisation of a bipartite web.

Potential for Apparent Competition

Flower visitation network from a meadow near Bristol, UK

Distance in a weighted network

Calculates discrepancy of a matrix

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

listModuleInformation

listModuleInformation

Indices of a bipartite network at the link level

Calculates the functional complementarity for the rows of a web

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

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

Converts a table of observations into a network matrix

Deletes empty rows and columns from a matrix.

Normalised degree, betweenness and closeness centrality

Analysis of bipartite webs at the level of the entire network

Flower visitation network from Melville Island, Northwest Territories, Canada

bipartite-package

Analysis of bipartite ecological webs

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

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

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

Detects compartments

A pollination network.

A spring flower visitation network from North Carolina, USA

Generate a random bipartite web

A flower visitation network from Urbana, IL, USA

Computes c and z for network modules

moduleWeb-class

Class "moduleWeb"

Compares observed pattern to random webs.

Secondary extinctions in bipartite networks

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

Generates null models for network analysis by considering external abundances

A pollination network.

Null model based on fitted marginal distribution

A pollination network.

decimalr2dtable

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

A pollination network from Northern Ellesmere Island, Canada

Generates null models for network analysis

Calculates any of several measures of nestedness

vazquez.example

Examples for some analyses

Robustness to species extinctions

Computes indices for a masked-one-mode network

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

Organise matrix by topology

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

Calculates the node-based specialisation index

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

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

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

printoutModuleInformation

printoutModuleInformation

Plot a matrix organised by topology

Shuffle web entries

olesen2002aigrettes

A flower visitation network from the Azores

Exports a tnet network to an igraph object

Null model with constrained connectance and moderately constrained marginal totals

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

Calculate various indices for network properties at the species level

Closeness centrality in a weighted network

slope.bipartite

Slope of extinction simulation

A pollination web from Argentina

Redefined clustering coefficient for two-mode networks

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

Log of bipartite versions and changes

Plotting function to visualize a bipartite food web

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

Computes end-point degrees for a bipartite network

Function to sort bipartite webs

A pollination network.

A pollination network.

A pollination network.

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

Flower visitation network

nestedcontribution

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

A pollination network from the Canadian Rockies

Computes species strength according to either of two definitions

Simulates extinction of a species from a bipartite network

A pollination network.

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

Calculates nestedness temperature of presence/absence matrices

olesen2002flores

Another flower visitation network from the Azores

Weighted-Interaction Nestedness Estimator

Creates null model for bipartite networks

Puts two or more webs into one array of webs

Calculate network dissimilarity (beta diversity) and its components

Conversion of a network matrix