Visualising Bipartite Networks and Calculating Some (Ecological) Indices
Reshape a webarray to a web X link matrix
Conversion of a network matrix
Ensures that networks conform to the tnet stardards
Calculate network dissimilarity (beta diversity) and its components
Betweenness centrality in a weighted network
Analysis of bipartite ecological webs
Calculates the (normalised) mean number of checkerboard combinations (...
Closeness centrality in a weighted network
Redefined clustering coefficient for two-mode networks
Detects compartments
computeModules
Computes c and z for network modules
Generates matrix with same marginal totals for non-negative decimal va...
Fits functions to cumulative degree distributions of both trophic leve...
Calculates standardised specialisation index d' (d prime) for each spe...
Calculates discrepancy of a matrix
Distance in a weighted network
Deletes empty rows and columns from a matrix.
Computes end-point degrees for a bipartite network
Simulates extinction of a species from a bipartite network
Calculates the functional complementarity for the rows of a web
Converts a table of observations into a network matrix
Generate a random bipartite web
Analysis of bipartite webs at the level of each of the two levels (gro...
Specialisation of a bipartite web.
Indices of a bipartite network at the link level
listModuleInformation
Generate simulated network according to a given probability matrix
Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"
Class "moduleWeb"
Normalised degree, betweenness and closeness centrality
Computes nestedness of a matrix as WNODA (and NODF and WNODF)
Calculates any of several measures of nestedness
Calculates the per-species contribution to nestedness (z-score relativ...
Calculates nestedness temperature of presence/absence matrices
Calculates the rank of a species in a matrix sorted for maximum nested...
Analysis of bipartite webs at the level of the entire network
Calculates the node-based specialisation index
Calculates the node overlap and separation according to Strona & Veech...
Computes indices for a masked-one-mode network
Null model based on fitted marginal distribution
Compares observed pattern to random webs.
Generates null models for network analysis
Potential for Apparent Competition
Paired Differences Index
Plot a matrix organised by topology
plotModuleWeb
Function to draw a circular plot to visualise potential apparent compe...
Visualize a bipartite interaction matrix (e.g. a foodweb)
Visualize a tripartite interaction matrix (e.g. a tritrophic foodweb)
printoutModuleInformation
Projecting binary and weighted two-mode networks onto weighted one-mod...
Generates null models for network analysis by considering external abu...
The restricted null model accounting for modules with nested entries
Robustness to species extinctions
Secondary extinctions in bipartite networks
Shuffle web entries
Slope of extinction simulation
Organise matrix by topology
Function to sort bipartite webs
Calculate various indices for network properties at the species level
Computes species strength according to either of two definitions
Creates null model for bipartite networks
Symmetrise_w
Exports a tnet network to an igraph object
Calculates the number of identical co-presences and co-absences for sp...
Calculates the variance-ratio as suggested by Schluter (1984)
Null model with constrained connectance and moderately constrained mar...
Examples for some analyses
Log of bipartite versions and changes
Plotting function to visualize a bipartite food web
Conversion of a network matrix into a (weighted) edge list
Puts two or more webs into one array of webs
Weighted-Interaction Nestedness Estimator
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.