Analysis of bipartite ecological webs

Description

Bipartite provides functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) networks, a.k.a. webs. It focusses on webs consisting of only two levels, e.g. pollinator-visitation 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.

Details

Input for most analyses is an interaction matrix of m species from one group (“higher”) with n species from another group (“lower”), i.e. a n x m matrix, where higher level species are in columns, lower level species in rows. Column and row names can be provided. This is fundamentally different from “one-mode” webs, which are organised as k x k matrix, i.e. one group of species only, in which each species can interact with each other. Such a format is incompatible with the functions we provide here. (Note, however, that functions as.one.mode and web2edges are convenience functions to morph bipartite networks into one-mode webs. Furthermore, some indices build on one-mode networks and are called from bipartite.)

Before you start with the network, you have to get the data into the right shape. The function frame2webs aims to facilitate this process. Arranging a web, e.g. by size, is supported by sortweb.

The typical first step is to visualise the network. 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). Both can be customised by many options.

The second step is to calculate indices describing network topography. There are three different levels this can be achieved at: the entire web (using function networklevel), at the level of each group (also using function networklevel) or the individual species (using function specieslevel). Most 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).

The third step is to compare results to null models. Many interaction matrices are very incomplete snapshots of the true underlying network (e.g. a one-week sampling of a pollination network on a patch of 4 x 4 meters). As a consequence, many species were rarely observed, many are singletons (only one recording). To make analyses comparable across networks with different sampling intensity and number of species per group, we need a common yardstick. We suggest that users should use a null model, i.e. an algorithm that randomises entries while constraining some web properties (such as dimensions, marginal totals or connectance). The function nullmodel provides a few such null models, but this is a wide field of research and we make no recommendations (actually, we do: see Dormann et al. 2009 and Dormann 2011, both shipping in the doc-folder of this package). You can also simulate networks using genweb or null.distr.

Finally, bipartite comes with 23 quantitative pollination network data sets taken from the NCEAS interaction webs data base (use data(package="bipartite") to show their names) and it has a few miscellaneous functions looking at some special features of bipartite networks (such as modularity: computeModules or apparent competition: PAC).

Speed: The code of bipartite is almost exclusively written in R. You can increase the speed a bit (by 30 to 50 %, depending on the functions you use) by compiling functions on-the-fly. To do so, you need to load the compiler package and type: enableJIT(3). The first time you call a function, it will be compiled to bytecode (just-in-time: jit), which takes a few seconds, but the second call will be substantially faster than without compilation. In the few tests we have run, this improvement was NOT substantial (i.e. a few tens of percent), indicating, I guess, that our R code wasn't too bad. See compiler-help files or http://www.r-statistics.com/2012/04/speed-up-your-r-code-using-a-just-in-time-jit-compiler/ for details.

See help pages for details and examples.

Package: bipartite
Type: Package
Version: 2.07
Date: 2016-07-11
License: GPL

versionlog

Please see help page versionlog for all changes and updates prior to version 2.00. This page will only list most recent changes.

Author(s)

Carsten F. Dormann, Jochen Fründ and Bernd Gruber, with additional code from many others (referred to in the respective help file), noticeably from Tore Opsahl's tnet package.

Maintainer: Carsten Dormann carsten.dormann@biom.uni-freiburg.de

References

Alarcon, R., Waser, N.M. and Ollerton, J. 2008. Year-to-year variation in the topology of a plant-pollinator interaction network. Oikos 117, 1796–1807

Almeida-Neto, M. and Ulrich, W. (2011) A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling & Software, 26, 173–178

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

Blüthgen, N., Menzel, F. and Blüthgen, N. (2006) Measuring specialization in species interaction networks. BMC Ecology 6, 12

Blüthgen, N., Menzel, F., Hovestadt, T., Fiala, B. and Blüthgen, N. (2007) Specialization, constraints, and conflicting interests in mutualistic networks. Current Biology 17, 1–6

Corso G., de Araújo 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. Martín González, 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

Devoto M., Bailey S., Craze P. & Memmott J. (2012) Understanding and planning ecological restoration of plant-pollinator networks. Ecology Letters 15, 319–328

Dormann, C.F., Fründ, J., Blüthgen, N., and Gruber, B. (2009) Indices, graphs and null models: analysing bipartite ecological networks. The Open Ecology Journal 2, 7–24

Dormann, C.F. (2011) How to be a specialist? Quantifying specialisation in pollination networks. Network Biology 1, 1–20

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]

Martín Gonzáles, A.M., Dalsgaard, B. and Olesen, J.M. (2009) Centrality measures and the importance of generalist species in pollination networks. Ecological Complexity, 7, 36–43

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

Morris, R. J., Lewis, O. T. and Godfray, H. C. J. (2004) Experimental evidence for apparent competition in a tropical forest food web. Nature 428, 310–313

Morris, R. J., Lewis, O. T. and Godfray, H. C. J. (2005) Apparent competition and insect community structure: towards a spatial perspective. Annales Zoologica Fennici 42, 449–462.

Müller, C. B., Adriaanse, I. C. T., Belshaw, R. and Godfray, H. C. J. (1999) The structure of an aphid-parasitoid community. Journal of Animal Ecology 68, 346–370

Poisot, T., Lepennetier, G., Martinez, E., Ramsayer, J., and Hochberg, M.E. (2011a) Resource availability affects the structure of a natural bacteria-bacteriophage community. Biology Letters 7, 201–204

Poisot, T., Bever, J.D., Nemri, A., Thrall, P.H., and Hochberg, M.E. (2011b) A conceptual framework for the evolution of ecological specialisation. Ecology Letters 14, 841–851

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

Vázquez, D. P. and Aizen, M. A. (2004) Asymmetric specialization: A pervasive feature of plant-pollinator interactions. Ecology 85, 1251–1257

Vázquez, D.P., Chacoff, N.,P. and Cagnolo, L. (2009) Evaluating multiple determinants of the structure of plant-animal mutualistic networks. Ecology 90, 2039–2046.

Examples

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Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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