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 |

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 |

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.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 |

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 |

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 web |

fd | Calculates the functional complementarity for the rows of a web |

frame2webs | Converts a table of observations into a network matrix |

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 |

H2fun | Specialisation of a bipartite web. |

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 |

junker2013 | Flower visitation network |

kato1990 | No. of individuals caught in a pollination web of a Japanese beech forest |

kevan1970 | A pollination network from Northern Ellesmere Island, Canada |

linklevel | Indices of a bipartite network at the link level |

listModuleInformation | listModuleInformation |

LPA_wb_plus | Functions "LPA_wb_plus" and "DIRT_LPA_wb_plus" |

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 |

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 |

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 |

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. |

quant2bin | Examples for some analyses |

r2dexternal | Generates null models for network analysis by considering external abundances |

readModuleData | computeModules |

robustness | Robustness to species extinctions |

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 |

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.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 |

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) |