I'm working with some data where I have a matrix of environmental variables and two matrices of presence-absence data; one for a set of zooplankton species and one for a set of macroinvertebrates. I have been using ordination and variation partitioning to look at the explanatory power of the environmental variables to each of the two biological matrices, but am looking for some interesting ways to visualize/examine the co-occurrence of macroinvertebrate species with zooplankton species under varying environmental conditions.
hello Amanda, Werner Ulrich is master in this area. There numerous papers about it but I think you can try to play with a program dealing with various aspects of co-occurrence
http://www.keib.umk.pl/wp-content/uploads/2013/04/PairsManual.pdf
good luck
take a look to EcoSim. Some years ago it was a free software. At the moment it's not. But you can find a R-version on Gotelli web page. I've never tried it but you can try!
http://www.uvm.edu/~ngotelli/homepage.html
Hi Amanda and Mattia,
the EcoSim would be a good choice. If you do not know the R statistics, than you may use the old version of EcoSim - the most recent free version that represents the original programming effort is still works fine and you can find it on Nick Gotelli's website (where the new R-version is), just crol down the page and you will find the "Original EcoSim update" - this version is relatively easy to use.
http://www.uvm.edu/~ngotelli/EcoSim/EcoSim.html
Hi all,
Ecosim and vegan package in R are all good options, but the several metrics for co-occurrence are only for each matrix. You may investigate possible evidence of competitive exclusion between zooplancton or macroinvertebrates, but not correlative patterns between those two matrices. If your aim is describe correlation patterns of the 3 matrices at the same time, I suggest take a look in the 4-corner analysis approach:
here: https://www.researchgate.net/publication/250076886_TESTING_THE_SPECIES_TRAITSENVIRONMENT_RELATIONSHIPS_THE_FOURTH-CORNER_PROBLEM_REVISITED?ev=srch_pub
and here: https://www.researchgate.net/publication/230738224_Improved_testing_of_species_traits--environment_relationships_in_the_fourth-corner_problem?ev=srch_pub
You may also use Redundance Analysis (RDA) to investigate correlation between 2 or 3 matrices. Vegan also do this. The problem is that linear correlation between factors is a major premisse in RDA analysis, but rarely is the case in biological systems.
Article Testing the species traits environment relationships: The fo...
Article Improved testing of species traits-environment relationships...
Paris seems to have a number of nice features but I was not able to locate a site for downloading although in the manual it says that the program is freeware. Does anybody know where it can be downloaded from?
Elena, you may download it from Werner Ulrich's website:
http://www.keib.umk.pl/pairs/?lang=en
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