Computes the Paired Differences Index
PDI(web, normalise=TRUE, log=FALSE)A bipartite interaction web, i.e.~a matrix with higher (cols) and lower (rows) trophic levels.
Logical; divides for each species by the maximum of interactions. Thereby species can be compared among each other and values range between 0 and 1. Defaults to TRUE, which differs from Poisot et al. (2011a). Note that Tim Poisot also recommends the normalised computation as default.
logical; since number of interactions is often highly skewed, the log yields a more even spread of PDI-values across species. Defaults to FALSE.
Returns a vector with PDI values between 0 (perfect generalist) and 1 (perfect specialist).
There are many ways to skin a cat. This is a more recent addition proposed by Poisot et al. (2011a) and used for mutualistic network analysis by Poisot et al. (2011b). This function can be used alone or through specieslevel.
If P is interaction strength (typically interaction frequency or proportion depending on argument normalized), then PDI for this species is computed as:
sum(P1 - Pi) /(H-1),
where P1 is the highest number of interactions in a link, while Pi are the remaining values. H is the number of potential interactors (e.g. plant species if the target species is a pollinator).
Dormann, C.F. (2011) How to be a specialist? Quantifying specialisation in pollination networks. Network Biology 1, 1--20
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
Poisot, T., E. Canard, N. Mouquet, and M. E. Hochberg. 2012. A comparative study of ecological specialization estimators. Methods in Ecology and Evolution 3, 537--544. 10.1111/j.2041-210X.2011.00174.x
See also specieslevel.
# NOT RUN {
data(Safariland)
PDI(Safariland) # for pollinators
PDI(t(Safariland), log=TRUE) # for plants
# }
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