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bipartite (version 2.11)

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

install.packages('bipartite')

Monthly Downloads

4,957

Version

2.11

License

GPL

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Repository

https://github.com/biometry/bipartite

Maintainer

Carsten F Dormann

Last Published

July 11th, 2018

Functions in bipartite (2.11)

Detects compartments

Generate simulated network according to a given probability matrix

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

Deletes empty rows and columns from a matrix.

DIRT_LPA_wb_plus

Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

Converts a table of observations into a network matrix

Indices of a bipartite network at the link level

Generate a random bipartite web

A pollination network from Northern Ellesmere Island, Canada

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

moduleWeb-class

Class "moduleWeb"

nestedcontribution

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

Calculates nestedness temperature of presence/absence matrices

Plotting function to visualize a bipartite food web

Robustness to species extinctions

Computes end-point degrees for a bipartite network

A flower visitation network from Urbana, IL, USA

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

Log of bipartite versions and changes

Calculates the node-based specialisation index

Calculates discrepancy of a matrix

listModuleInformation

listModuleInformation

Distance in a weighted network

Simulates extinction of a species from a bipartite network

Flower visitation network from Melville Island, Northwest Territories, Canada

Flower visitation network from a meadow near Bristol, UK

Flower visitation network

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

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

Calculates the functional complementarity for the rows of a web

bipartite-package

Analysis of bipartite ecological webs

A spring flower visitation network from North Carolina, USA

Computes indices for a masked-one-mode network

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

olesen2002flores

Another flower visitation network from the Azores

A pollination network from the Canadian Rockies

Generates null models for network analysis

olesen2002aigrettes

A flower visitation network from the Azores

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

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

Calculates any of several measures of nestedness

Secondary extinctions in bipartite networks

Function to sort bipartite webs

slope.bipartite

Slope of extinction simulation

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

Shuffle web entries

Calculate various indices for network properties at the species level

Weighted-Interaction Nestedness Estimator

Computes species strength according to either of two definitions

Creates null model for bipartite networks

Generates null models for network analysis by considering external abundances

A pollination network.

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

A pollination network.

A pollination network.

A pollination network.

vazquez.example

Examples for some analyses

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

A pollination network.

Analysis of bipartite webs at the level of the entire network

A pollination network.

Null model based on fitted marginal distribution

Null model with constrained connectance and moderately constrained marginal totals

Compares observed pattern to random webs.

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

A pollination network.

printoutModuleInformation

printoutModuleInformation

Exports a tnet network to an igraph object

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

Puts two or more webs into one array of webs

Ensures that networks conform to the tnet stardards

A pollination web from Argentina

Normalised degree, betweenness and closeness centrality

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

Paired Differences Index

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

Potential for Apparent Competition

Specialisation of a bipartite web.

Conversion of a network matrix

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

Redefined clustering coefficient for two-mode networks

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.

Computes c and z for network modules

Individuals caught in a pollination web in boreal Canada.

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