bipartite (version 0.90)

bipartite-package: Analysis of bipartite ecological webs.

Description

Bipartite provides functions to viualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focusses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.

encoding

latin1

Details

We only had three types of bipartite webs in mind when writing this package: seed-disperser, plant-pollinator and predator-prey systems. In how far it makes sense to use these functionalities for other systems (or indeed for these systems) lies in the hands of the user. Please refer to the literature cited for details on the theory behind the indices. Input for most analyses is an interaction matrix of m higher level species with n lower level species, i.e. an n x m matrix, where higher trophic level species are in columns, lower level in rows. Column and row names can be provided. This is fundamentally different from multi-dimensional webs, which are organised as k x k matrix, i.e. each species against each other. Such a format is incompatible with the functions we provide here. The first step is to visualise the interaction web. Two functions are on offer here: one (visweb) simply plots the matrix in colours depicting the strength of an interaction and options for re-arranging columns and rows (e.g. to identify compartments or nesting). The other function (plotweb) plots the actual web with participants (as two rows of rectangles) connected by lines (proportional to interaction strength). The second step is to calculate various indices describing network topography. There are two different levels this can be achieved at: the entire web (using function networklevel) or the individual species (using function specieslevel). All other functions in the package are helpers, although some can be called on their own and return the respective result (dfun, H2fun and second.extinct with slope.bipartite). See function description for details and examples. ll{ Package: bipartite Type: Package Version: 0.90 Date: 2009-03-24 License: GPL }

References

Bascompte, J., Jordano, P. and Olesen, J. M. (2006) Asymmetric coevolutionary networks facilitate biodiversity maintenance. Science 312, 431--433 Bersier, L. F., Banasek-Richter, C. and Cattin, M. F. (2002) Quantitative descriptors of food-web matrices. Ecology 83, 2394--2407 Bl�thgen, N., Menzel, F. and Bl�thgen, N. (2006) Measuring specialization in species interaction networks. BMC Ecology 6, 12 Bl�thgen, N., Menzel, F., Hovestadt, T., Fiala, B. and Bl�thgen, N. (2007) Specialization, constraints, and conflicting interests in mutualistic networks. Current Biology 17, 1--6 Corso G., de Ara�jo A.I.L. and de Almeida A.M. (2008) A new nestedness estimator in community networks. arXiv, 0803.0007v1 [physics.bio-ph] Dalsgaard, B., A. M. Mart�n Gonz�lez, J. M. Olesen, A. Timmermann, L. H. Andersen, and J. Ollerton. (2008) Pollination networks and functional specialization: a test using Lesser Antillean plant-hummingbird assemblages. Oikos 117, 789--793 Dormann, C.F., Fr�nd, J., Bl�thgen, N., and Gruber, B. (2009) Indices, graphs and null models: analysing bipartite ecological networks. The Open Ecology Journal 2, 7--24.. Galeano J., Pastor J.M. and Iriondo J.M. (2008) Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices. arXiv 0808.3397v1 [physics.bio-ph] 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 Tylianakis, J. M., Tscharntke, T. and Lewis, O. T. (2007) Habitat modification alters the structure of tropical host-parasitoid food webs. Nature 445, 202--205 Vazquez, D. P. and Aizen, M. A. (2004) Asymmetric specialization: A pervasive feature of plant-pollinator interactions. Ecology 85, 1251--1257 Vazquez, P.D., Chacoff, N.,P. and Cagnolo, L. (2009) Evaluating multiple determinants of the structure of plant-animal mutualistic networks. Ecology in press.

Examples

data(Safariland)
plotweb(Safariland)
visweb(Safariland)
networklevel(Safariland)
specieslevel(Safariland)