Dark diversity is a set of species that are absent from a sample but are likely to occur in that sample as these species often co-occur with the observed species in other locations.
Written by Meelis Pärtel, Macroecology workgroup at the University of Tartumeelis.email@example.com http://www.botany.ut.ee/macroecology/en
For more information about dark diversity calculation from co-occurrences and for citing this application please use this reference:Lewis, R. J., Szava‐Kovats, R. and Pärtel, M. (2015) Estimating dark diversity and species pools: An empirical assessment of two methods. Methods in Ecology and Evolution.
For larger datasets (>1000 samples or species) I recommend that you use the R script provided as supplementary material for the paper.
This method has also been used in our other recent studies:Ronk, A., Szava-Kovats, R., Pärtel, M. (2015) Applying the dark diversity concept to plants at the European scale. Ecography (Online Early). Riibak, K., Reitalu, T., Tamme, R., Helm, A., Gerhold, P., Znamenskiy, S., Bengtsson, K., Rosén, E., Prentice, H. C., Pärtel, M. (2015) Dark diversity in dry calcareous grasslands is determined by dispersal ability and stress-tolerance. Ecography 38, 713-721.
This web app uses Shiny, a web application framework for R:http://shiny.rstudio.com/