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bipartite (version 2.16)

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

4,003

Version

2.16

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

February 4th, 2021

Functions in bipartite (2.16)

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

Reshape a webarray to a web X link matrix

Specialisation of a bipartite web.

Normalised degree, betweenness and closeness centrality

Paired Differences Index

A pollination web from Argentina

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

Potential for Apparent Competition

Conversion of a network matrix

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

Ensures that networks conform to the tnet stardards

Individuals caught in a pollination web in boreal Canada.

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

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

Converts a table of observations into a network matrix

Calculates the functional complementarity for the rows of a web

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

Indices of a bipartite network at the link level

Simulates extinction of a species from a bipartite network

Computes end-point degrees for a bipartite network

bipartite-package

Analysis of bipartite ecological webs

Calculate network dissimilarity (beta diversity) and its components

listModuleInformation

listModuleInformation

Closeness centrality in a weighted network

Detects compartments

Calculates nestedness temperature of presence/absence matrices

nestedcontribution

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

Redefined clustering coefficient for two-mode networks

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

Deletes empty rows and columns from a matrix.

Generate a random bipartite web

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

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

Calculates discrepancy of a matrix

Calculates the node-based specialisation index

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

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

A flower visitation network from Urbana, IL, USA

Organise matrix by topology

printoutModuleInformation

printoutModuleInformation

Distance in a weighted network

Betweenness centrality in a weighted network

Computes indices for a masked-one-mode network

A pollination network.

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

A pollination network.

Secondary extinctions in bipartite networks

Null model with constrained connectance and moderately constrained marginal totals

Calculate various indices for network properties at the species level

Calculates any of several measures of nestedness

Flower visitation network from a meadow near Bristol, UK

olesen2002aigrettes

A flower visitation network from the Azores

Function to sort bipartite webs

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

Flower visitation network

A pollination network.

Generates null models for network analysis

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

Computes c and z for network modules

A pollination network.

A pollination network from Northern Ellesmere Island, Canada

A pollination network.

A spring flower visitation network from North Carolina, USA

Weighted-Interaction Nestedness Estimator

Generate simulated network according to a given probability matrix

Flower visitation network from Melville Island, Northwest Territories, Canada

Null model based on fitted marginal distribution

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

vazquez.example

Examples for some analyses

Puts two or more webs into one array of webs

decimalr2dtable

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

Generates null models for network analysis by considering external abundances

Analysis of bipartite webs at the level of the entire network

Plot a matrix organised by topology

moduleWeb-class

Class "moduleWeb"

Compares observed pattern to random webs.

olesen2002flores

Another flower visitation network from the Azores

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

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

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

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

A pollination network from the Canadian Rockies

Robustness to species extinctions

Shuffle web entries

Computes species strength according to either of two definitions

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

Creates null model for bipartite networks

slope.bipartite

Slope of extinction simulation

A pollination network.

A pollination network.

Exports a tnet network to an igraph object

Plotting function to visualize a bipartite food web

Log of bipartite versions and changes