Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Documentation for package ‘bipartite’ version 2.20

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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

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 --

edgelist2webs	Converts a table of observations into a network matrix
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)
PosteriorProb	The restricted null model accounting for modules with nested entries
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
restrictednull	The restricted null model accounting for modules with nested entries
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)