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**bipartite**: Visualising Bipartite Networks and Calculating Some (Ecological) Indices**extinction**: Simulates extinction of a species from a bipartite network

# Simulates extinction of a species from a bipartite network

### Description

Following (how I remember) the paper of Memmott et al. (2004), this function deletes a column (e.g. pollinator) or row (e.g. plant). Only a helper function for `second.extinct`

, really.

### Usage

1 2 | ```
extinction(web, participant = "both", method = "random", ext.row=NULL,
ext.col=NULL)
``` |

### Arguments

`web` |
A matrix representing the interactions observed between higher trophic level species (columns) and lower trophic level species (rows). Usually this will be number of pollinators on each species of plants or number of parasitoids on each species of prey. |

`participant` |
Which level of participant to remove: lower removes a row, higher removes a row, both randomly picks either row or column. |

`method` |
Determines sequence of extinctions: random removes a random participant, while abundance removes the least abundant species first. external will use the externally provided vector to determine extinction sequence. |

`ext.row` |
Optional vector giving the sequence in which lower-level species are to be deleted. |

`ext.col` |
Optional vector giving the sequence in which higher-level species are to be deleted. |

### Details

In itself rather useless. Called repeatedly by `second.extinct`

to build an extinction sequence and accordingly a sequence of secondary extinctions.

### Value

Returns the same matrix that was given as object, just with one row or column being turned into zeros.

### Author(s)

Carsten F. Dormann

### References

Memmott, J., Waser, N. M. and Price, M. V. 2004 Tolerance of pollination networks to species extinctions. *Proceedings of the Royal Society B* **271**, 2605–2611

### See Also

`second.extinct`

### Examples

1 2 3 4 5 6 | ```
## Not run:
data(Safariland)
(w <- extinction(Safariland, participant="lower", method="abun"))
empty(w, count=TRUE)
## End(Not run)
``` |

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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