bipartite (version 2.05)

second.extinct: Secondary extinctions in bipartite networks

Description

Calculates the consequences of removing a species from a bipartite network. With plotting and slope-estimation functionality.

Usage

second.extinct(web, participant = "higher", method = "abun", nrep = 10,
  details = FALSE, ext.row=NULL, ext.col=NULL)

Arguments

web

Web is 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

participant

high (default) or low or both, depending if you want to exterminate higher trophic level species, lower trophic level species, or randomly choose species of both levels.

method

Random deletion of a species (random); according to its abundance, with least abundant going extinct first (abundance; default) or "degree" to build a sequence from the best-to-least connected species. Th

nrep

Number of replicates of extermination sequence. Will not be considered for method abundance.

details

Logical; returns details, i.e. for each replicate the sequence of secondary extinctions. If set to FALSE (default), replicated runs will be averaged. Using anything but FALSE will not yield the correct object for further analysi

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.

Value

• Function returns an object of class bipartite to ensure proper working of function plot.bipartite.

  If details=FALSE, the returned object contains a matrix with columns representing the number of species going extinct from one step to the next, averaged across all runs.

  If details=FALSE, the returned object will be a list of matrices containing the number of species going extinct at each step.

  The objects attribute exterminated gives the name of the trophic level (pollinator or plant).

Details

The procedure of this function is simple. For example imagine the web to represent a pollination web, in which pollinators die one by one. Set all entries of a column to zero, see how may rows are now also all-zero (i.e. species that are now not pollinated any more), and count these as secondary extinctions of the primary exterminated pollinator.

Internally, each extermination is achieved by a call to extinction, followed by a call to empty, which counts the number of all-zero columns and rows.

Although written for pollination webs (hence the nomenclature of pollinator and plant), it can be similarly applied to other types of bipartite networks. It is called by networklevel.

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

networklevel calls second.extinct; extinction and empty are internal helper functions, and slope.bipartite calculates extinction slopes from the output of second.extinct.

Examples

data(Safariland)
(ex <- second.extinct(Safariland, participant="lower", method="random", nrep=50, 
	details=TRUE))
(ex <- second.extinct(Safariland, participant="lower", method="random", nrep=50, 
	details=FALSE))