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**bipartite**: Visualising Bipartite Networks and Calculating Some (Ecological) Indices**clustering_tm**: Redefined clusering coefficient for two-mode networks

# Redefined clusering coefficient for two-mode networks

### Description

This function calculates the two-mode clusering coefficient as proposed by Opsahl (2010).

Note: If you are having problems with this function (i.e., run out of memory or it being slow for simulations), there is a quicker and much more memory efficient c++ function. However, this function is not fully integrated in R, and requires a few extra steps. Send me an email to get the source-code and Windows-compiled files.

### Usage

1 | ```
clustering_tm(net, subsample=1, seed=NULL)
``` |

### Arguments

`net` |
A binary or weighted two-mode edgelist |

`subsample` |
Whether a only a subset of 4-paths should we used when calculating the measure. This is particularly useful when running out of memory analysing large networks. If it is set to 1, all the 4-paths are analysed. If it set to a value below one, this is roughly the proportion of 4-paths that will be analysed. If it is set to an interger greater than 1, this number of ties that form the first part of a 4-path that will be analysed. Note: The c++ functions are better as they analyse the full network. |

`seed` |
If a subset of 4-paths is analysed, by setting this parameter, the results are reproducable. |

### Value

Returns the outcome of the equation presented in the paper

### Note

version 1.0.0, taken, with permission, from package tnet

### Author(s)

Tore Opsahl; http://toreopsahl.com

### References

Opsahl, T. 2010. Triadic closure in two-mode networks: Redefining the global and local clustering coefficients. *arXiv*,1006.0887

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- as.one.mode: Conversion of a network matrix
- as.one.mode: Conversion of a network matrix
- as.tnet: Ensures that networks conform to the tnet stardards
- as.tnet: Ensures that networks conform to the tnet stardards
- barrett1987: Individuals caught in a pollination web in boreal Canada.
- barrett1987: Individuals caught in a pollination web in boreal Canada.
- betweenness_w: Betweenness centrality in a weighted network
- betweenness_w: Betweenness centrality in a weighted network
- bezerra2009: Individuals observed in a flower-visitation network of...
- bezerra2009: Individuals observed in a flower-visitation network of...
- bipartite-package: Analysis of bipartite ecological webs
- bipartite-package: Analysis of bipartite ecological webs
- closeness_w: Closeness centrality in a weighted network
- closeness_w: Closeness centrality in a weighted network
- clustering_tm: Redefined clusering coefficient for two-mode networks
- clustering_tm: Redefined clusering coefficient for two-mode networks
- compart: Detects compartments
- compart: Detects compartments
- computeModules: Function "computeModules"
- computeModules: Function "computeModules"
- C.score: Calculates the (normalised) mean number of checkerboard...
- C.score: Calculates the (normalised) mean number of checkerboard...
- czvalues: Computes c and z for network modules
- czvalues: Computes c and z for network modules
- degreedistr: Fits functions to cumulative degree distributions of both...
- degreedistr: Fits functions to cumulative degree distributions of both...
- dfun: Calculates standardised specialisation index d' (d prime) for...
- dfun: Calculates standardised specialisation index d' (d prime) for...
- discrepancy: Calculates discrepancy of a matrix
- discrepancy: Calculates discrepancy of a matrix
- distance_w: Distance in a weighted network
- distance_w: Distance in a weighted network
- elberling1999: No. of visits in a pollination web of arctic-alpine Sweden
- elberling1999: No. of visits in a pollination web of arctic-alpine Sweden
- empty: Deletes empty rows and columns from a matrix.
- empty: Deletes empty rows and columns from a matrix.
- endpoint: Computes end-point degrees for a bipartite network
- endpoint: Computes end-point degrees for a bipartite network
- extinction: Simulates extinction of a species from a bipartite network
- extinction: Simulates extinction of a species from a bipartite network
- fc: Calculates the functional complementarity for the rows of a...
- fc: Calculates the functional complementarity for the rows of a...
- frame2webs: Converts a table of observations into a network matrix
- 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...
- grouplevel: Analysis of bipartite webs at the level of each of the two...
- H2fun: Specialisation of a bipartite web.
- H2fun: Specialisation of a bipartite web.
- inouye1988: A pollination network from the Snowy Mountains of New South...
- inouye1988: A pollination network from the Snowy Mountains of New South...
- junker2013: Flower visitation network
- junker2013: Flower visitation network
- kato1990: No. of individuals caught in a pollination web of a Japanese...
- kato1990: No. of individuals caught in a pollination web of a Japanese...
- kevan1970: A pollination network from Northern Ellesmere Island, Canada
- kevan1970: A pollination network from Northern Ellesmere Island, Canada
- linklevel: Indices of a bipartite network at the link level
- linklevel: Indices of a bipartite network at the link level
- listModuleInformation: Function "listModuleInformation"
- listModuleInformation: Function "listModuleInformation"
- memmott1999: Flower visitation network from a meadow near Bristol, UK
- memmott1999: Flower visitation network from a meadow near Bristol, UK
- mgen: Generate simulated network according to a given probability...
- mgen: Generate simulated network according to a given probability...
- moduleWeb-class: Class "moduleWeb"
- moduleWeb-class: Class "moduleWeb"
- mosquin1967: Flower visitation network from Melville Island, Northwest...
- mosquin1967: Flower visitation network from Melville Island, Northwest...
- motten1982: A spring flower visitation network from North Carolina, USA
- motten1982: A spring flower visitation network from North Carolina, USA
- nested: Calculates any of several measures of nestedness
- nested: Calculates any of several measures of nestedness
- nestedcontribution: Calculates the per-species contribution to nestedness...
- nestedcontribution: Calculates the per-species contribution to nestedness...
- nestedness: Calculates nestedness temperature of presence/absence...
- nestedness: Calculates nestedness temperature of presence/absence...
- nestedrank: Calculates the rank of a species in a matrix sorted for...
- nestedrank: Calculates the rank of a species in a matrix sorted for...
- networklevel: Analysis of bipartite webs at the level of the entire network
- networklevel: Analysis of bipartite webs at the level of the entire network
- nodespec: Calculates the node-based specialisation index
- nodespec: Calculates the node-based specialisation index
- npartite: Computes indices for a masked-one-mode network
- npartite: Computes indices for a masked-one-mode network
- null.distr: Null model based on fitted marginal distribution
- null.distr: Null model based on fitted marginal distribution
- null.t.test: Compares observed pattern to random webs.
- null.t.test: Compares observed pattern to random webs.
- olesen2002aigrettes: A flower visitation network from the Azores
- olesen2002aigrettes: A flower visitation network from the Azores
- olesen2002flores: Another flower visitation network from the Azores
- olesen2002flores: Another flower visitation network from the Azores
- ollerton2003: ollerton2003
- ollerton2003: ollerton2003
- PDI: Paired Differences Index
- PDI: Paired Differences Index
- plotModuleWeb: Function "plotModuleWeb"
- plotModuleWeb: Function "plotModuleWeb"
- plotPAC: Function to draw a circular plot to visualise potential...
- plotPAC: Function to draw a circular plot to visualise potential...
- plotweb: Visualize a bipartite interaction matrix (e.g. a foodweb)
- plotweb: Visualize a bipartite interaction matrix (e.g. a foodweb)
- printoutModuleInformation: Function printoutModuleInformation
- printoutModuleInformation: Function printoutModuleInformation
- projecting_tm: Projecting binary and weighted two-mode networks onto...
- projecting_tm: Projecting binary and weighted two-mode networks onto...
- r2dexternal: Generates null models for network analysis by considering...
- r2dexternal: Generates null models for network analysis by considering...
- Safariland: A pollination web from Argentina
- Safariland: A pollination web from Argentina
- schemske1978: A flower visitation network from Urbana, IL, USA
- schemske1978: A flower visitation network from Urbana, IL, USA
- second.extinct: Secondary extinctions in bipartite networks
- second.extinct: Secondary extinctions in bipartite networks
- shuffle.web: Shuffle web entries
- shuffle.web: Shuffle web entries
- slope.bipartite: Slope of extinction simulation
- slope.bipartite: Slope of extinction simulation
- small1976: A flower visitation network from a peat bog in Ottawa, Canada
- small1976: A flower visitation network from a peat bog in Ottawa, Canada
- sortweb: Function to sort bipartite webs
- sortweb: Function to sort bipartite webs
- specieslevel: Calculate various indices for network properties at the...
- specieslevel: Calculate various indices for network properties at the...
- strength: Computes species strength according to either of two...
- strength: Computes species strength according to either of two...
- swap.web: Creates null model for bipartite networks
- swap.web: Creates null model for bipartite networks
- symmetrise_w: Symmetrise_w
- symmetrise_w: Symmetrise_w
- tnet_igraph: Exports a tnet network to an igraph object
- tnet_igraph: Exports a tnet network to an igraph object
- togetherness: Calculates the number of identical co-presences and...
- togetherness: Calculates the number of identical co-presences and...
- vazarr: A pollination network.
- vazarr: A pollination network.
- vazcer: A pollination network.
- vazcer: A pollination network.
- vazllao: A pollination network.
- vazllao: A pollination network.
- vazmasc: A pollination network.
- vazmasc: A pollination network.
- vazmasnc: A pollination network.
- vazmasnc: A pollination network.
- vazquec: A pollination network.
- vazquec: A pollination network.
- vazquenc: A pollination network.
- vazquenc: A pollination network.
- versionlog: Log of bipartite versions and changes
- versionlog: Log of bipartite versions and changes
- visweb: Plotting function to visualize a bipartite food web
- visweb: Plotting function to visualize a bipartite food web
- V.ratio: Calculates the variance-ratio as suggested by Schluter (1984)
- V.ratio: Calculates the variance-ratio as suggested by Schluter (1984)
- web2edges: Conversion of a network matrix into a (weighted) edge list
- web2edges: Conversion of a network matrix into a (weighted) edge list
- webs2array: Puts two or more webs into one array of webs
- webs2array: Puts two or more webs into one array of webs