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.
|Author||Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Mariano Devoto, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones|
|Date of publication||2016-11-08 11:49:49|
|Maintainer||Carsten F. Dormann <firstname.lastname@example.org>|
as.one.mode: Conversion of a network matrix
as.tnet: Ensures that networks conform to the tnet stardards
barrett1987: Individuals caught in a pollination web in boreal Canada.
betweenness_w: Betweenness centrality in a weighted network
bezerra2009: Individuals observed in a flower-visitation network of...
bipartite-package: Analysis of bipartite ecological webs
closeness_w: Closeness centrality in a weighted network
clustering_tm: Redefined clusering coefficient for two-mode networks
compart: Detects compartments
computeModules: Function "computeModules"
C.score: Calculates the (normalised) mean number of checkerboard...
czvalues: Computes c and z for network modules
degreedistr: Fits functions to cumulative degree distributions of both...
dfun: Calculates standardised specialisation index d' (d prime) for...
discrepancy: Calculates discrepancy of a matrix
distance_w: Distance in a weighted network
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
fc: Calculates the functional complementarity for the rows of a...
frame2webs: Converts a table of observations into a network matrix
genweb: Generate a random bipartite web
grouplevel: Analysis of bipartite webs at the level of each of the two...
H2fun: Specialisation of a bipartite web.
inouye1988: A pollination network from the Snowy Mountains of New South...
junker2013: Flower visitation network
kato1990: No. of individuals caught in a pollination web of a Japanese...
kevan1970: A pollination network from Northern Ellesmere Island, Canada
linklevel: Indices of a bipartite network at the link level
listModuleInformation: Function "listModuleInformation"
memmott1999: Flower visitation network from a meadow near Bristol, UK
mgen: Generate simulated network according to a given probability...
moduleWeb-class: Class "moduleWeb"
mosquin1967: Flower visitation network from Melville Island, Northwest...
motten1982: A spring flower visitation network from North Carolina, USA
nested: Calculates any of several measures of nestedness
nestedcontribution: Calculates the per-species contribution to nestedness...
nestedness: Calculates nestedness temperature of presence/absence...
nestedrank: Calculates the rank of a species in a matrix sorted for...
networklevel: Analysis of bipartite webs at the level of the entire network
nodespec: Calculates the node-based specialisation index
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.
olesen2002aigrettes: A flower visitation network from the Azores
olesen2002flores: Another flower visitation network from the Azores
PDI: Paired Differences Index
plotModuleWeb: Function "plotModuleWeb"
plotPAC: Function to draw a circular plot to visualise potential...
plotweb: Visualize a bipartite interaction matrix (e.g. a foodweb)
printoutModuleInformation: Function printoutModuleInformation
projecting_tm: Projecting binary and weighted two-mode networks onto...
r2dexternal: Generates null models for network analysis by considering...
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
sortweb: Function to sort bipartite webs
specieslevel: Calculate various indices for network properties at the...
strength: Computes species strength according to either of two...
swap.web: Creates null model for bipartite networks
tnet_igraph: Exports a tnet network to an igraph object
togetherness: Calculates the number of identical co-presences and...
vazarr: A pollination network.
vazcer: A pollination network.
vazllao: A pollination network.
vazmasc: A pollination network.
vazmasnc: A pollination network.
vazquec: A pollination network.
vazquenc: A pollination network.
versionlog: Log of bipartite versions and changes
visweb: Plotting function to visualize a bipartite food web
V.ratio: Calculates the variance-ratio as suggested by Schluter (1984)
web2edges: Conversion of a network matrix into a (weighted) edge list
webs2array: Puts two or more webs into one array of webs