Visualising Bipartite Networks and Calculating Some (Ecological) Indices


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Documentation for package ‘bipartite’ version 2.16

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A B C D E F G H I J K L M N O P Q R S T V W

bipartite-package Analysis of bipartite ecological webs

-- A --

addEmptyColToMatrix plotModuleWeb
addEmptyRowToMatrix plotModuleWeb
array2linkmx Reshape a webarray to a web X link matrix
as.one.mode Conversion of a network matrix
as.tnet Ensures that networks conform to the tnet stardards

-- B --

barrett1987 Individuals caught in a pollination web in boreal Canada.
BC Normalised degree, betweenness and closeness centrality
betalinkr Calculate network dissimilarity (beta diversity) and its components
betalinkr_multi Calculate network dissimilarity (beta diversity) and its components
betweenness_w Betweenness centrality in a weighted network
bezerra2009 Individuals observed in a flower-visitation network of oil-collecting bees in a Brazilian steppe.
bipartite Analysis of bipartite ecological webs

-- C --

C.score Calculates the (normalised) mean number of checkerboard combinations (C-score) in a matrix
CC Normalised degree, betweenness and closeness centrality
closeness_w Closeness centrality in a weighted network
clustering_tm Redefined clustering coefficient for two-mode networks
compart Detects compartments
computeModules computeModules
confint Examples for some analyses
convert2moduleWeb Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"
czvalues Computes c and z for network modules

-- D --

decimalr2dtable Generates matrix with same marginal totals for non-negative decimal values
degreedistr Fits functions to cumulative degree distributions of both trophic levels of a network.
dfun Calculates standardised specialisation index d' (d prime) for each species in the lower trophic level of a bipartite network.
DIRT_LPA_wb_plus Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"
discrepancy Calculates discrepancy of a matrix
distance_w Distance in a weighted network
drawModules plotModuleWeb

-- E --

elberling1999 No. of visits in a pollination web of arctic-alpine Sweden
empty Deletes empty rows and columns from a matrix.
endpoint Computes end-point degrees for a bipartite network
extinction Simulates extinction of a species from a bipartite network

-- F --

fc Calculates the functional complementarity for the rows of a web
fd Calculates the functional complementarity for the rows of a web
frame2webs Converts a table of observations into a network matrix

-- G --

genweb Generate a random bipartite web
getModuleCoordinates plotModuleWeb
grouplevel Analysis of bipartite webs at the level of each of the two levels (groups) of the network

-- H --

H2fun Specialisation of a bipartite web.

-- I --

inouye1988 A pollination network from the Snowy Mountains of New South Wales, Australia
intasymm Examples for some analyses
intereven Examples for some analyses
isCorrectModuleWebObject plotModuleWeb

-- J --

junker2013 Flower visitation network

-- K --

kato1990 No. of individuals caught in a pollination web of a Japanese beech forest
kevan1970 A pollination network from Northern Ellesmere Island, Canada

-- L --

linklevel Indices of a bipartite network at the link level
listModuleInformation listModuleInformation
LPA_wb_plus Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus"

-- M --

memmott1999 Flower visitation network from a meadow near Bristol, UK
metaComputeModules computeModules
mgen Generate simulated network according to a given probability matrix
mlik Examples for some analyses
module2constraints Computes nestedness of a matrix as WNODA (and NODF and WNODF)
moduleWeb-class Class "moduleWeb"
mosquin1967 Flower visitation network from Melville Island, Northwest Territories, Canada
motten1982 A spring flower visitation network from North Carolina, USA

-- N --

ND Normalised degree, betweenness and closeness centrality
nest.smdm Computes nestedness of a matrix as WNODA (and NODF and WNODF)
nested Calculates any of several measures of nestedness
nestedcontribution Calculates the per-species contribution to nestedness (z-score relative to null model)
nestedness Calculates nestedness temperature of presence/absence matrices
nestedrank Calculates the rank of a species in a matrix sorted for maximum nestedness
netstats Examples for some analyses
networklevel Analysis of bipartite webs at the level of the entire network
nodespec Calculates the node-based specialisation index
NODF Computes nestedness of a matrix as WNODA (and NODF and WNODF)
NOS Calculates the node overlap and separation according to Strona & Veech (2015)
npartite Computes indices for a masked-one-mode network
null.distr Null model based on fitted marginal distribution
null.t.test Compares observed pattern to random webs.
nullmodel Generates null models for network analysis

-- O --

olesen2002aigrettes A flower visitation network from the Azores
olesen2002flores Another flower visitation network from the Azores
olito2015 A pollination network from the Canadian Rockies
ollerton2003 ollerton2003
one.grouplevel Analysis of bipartite webs at the level of each of the two levels (groups) of the network

-- P --

PAC Potential for Apparent Competition
PDI Paired Differences Index
plot.wine Weighted-Interaction Nestedness Estimator
plotmat Examples for some analyses
plotmatrix Plot a matrix organised by topology
plotModuleWeb plotModuleWeb
plotPAC Function to draw a circular plot to visualise potential apparent competition (PAC)
plotweb Visualize a bipartite interaction matrix (e.g. a foodweb)
plotweb2 Visualize a tripartite interaction matrix (e.g. a tritrophic foodweb)
prepareWebForPlottingModules plotModuleWeb
printoutModuleInformation printoutModuleInformation
projecting_tm Projecting binary and weighted two-mode networks onto weighted one-mode networks.

-- Q --

quant2bin Examples for some analyses

-- R --

r2dexternal Generates null models for network analysis by considering external abundances
readModuleData computeModules
robustness Robustness to species extinctions

-- S --

Safariland A pollination web from Argentina
schemske1978 A flower visitation network from Urbana, IL, USA
second.extinct Secondary extinctions in bipartite networks
shuffle.web Shuffle web entries
slope.bipartite Slope of extinction simulation
small1976 A flower visitation network from a peat bog in Ottawa, Canada
sortmatr Examples for some analyses
sortmatrext Examples for some analyses
sortmatrix Organise matrix by topology
sortweb Function to sort bipartite webs
specieslevel Calculate various indices for network properties at the species level
strength Computes species strength according to either of two definitions
swap.web Creates null model for bipartite networks
symmetrise_w Symmetrise_w

-- T --

tnet_igraph Exports a tnet network to an igraph object
togetherness Calculates the number of identical co-presences and co-absences for species-on-islands

-- V --

V.ratio Calculates the variance-ratio as suggested by Schluter (1984)
vazarr A pollination network.
vazcer A pollination network.
vazllao A pollination network.
vazmasc A pollination network.
vazmasnc A pollination network.
vaznull Null model with constrained connectance and moderately constrained marginal totals
vaznullexternal Generates null models for network analysis by considering external abundances
vazquec A pollination network.
vazquenc A pollination network.
vazquez.example Examples for some analyses
versionlog Log of bipartite versions and changes
visweb Plotting function to visualize a bipartite food web

-- W --

web2edges Conversion of a network matrix into a (weighted) edge list
webs2array Puts two or more webs into one array of webs
wine Weighted-Interaction Nestedness Estimator
WNODA Computes nestedness of a matrix as WNODA (and NODF and WNODF)
WNODF Computes nestedness of a matrix as WNODA (and NODF and WNODF)