Visualising Bipartite Networks and Calculating Some (Ecological)
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Documentation for package ‘bipartite’ version 2.22
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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 --
| 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 --
| massaction | Calculates the spectral radius as a nestedness measurement of a bipartite matrix, possibly with regard to mass action |
| 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) |
| plotweb_deprecated | Visualize a bipartite interaction matrix (e.g. a 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 |
| spectral.radius | Calculates the spectral radius as a nestedness measurement of a bipartite matrix, possibly with regard to mass action |
| 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) |