If I want to execute null model analysis by using R statistical software to understand deterministic community assembly pattern, then from which package could I get best outcome?
The "vegan" package may have the tools you're looking for.
http://vegan.r-forge.r-project.org/
Hi Patrick,
Thanks to you. I have already used vegan package to execute null model analysis. but in that package, it is suggested to use only species presence-absence matrix for this analysis. I can not understand how to interpret community assembly pattern from this analysis by using species presence-absence data only.
check out permatfull and permatswap functions, also there is a lot more nullmodel stuff coming up in the devel version at R-Forge: https://r-forge.r-project.org/projects/vegan/
My apologies for the redundant suggestion about the "vegan" package. I'm not a community ecologist, so admittedly I'm out of my comfort zone here. So, I'm shooting blind here! I did get curious and found this R code used in a paper by Nathan Kraft. It seems to use abundance data (not simply presence/absence)...
http://life.umd.edu/biology/kraftlab/Code_files/community_assembly.R
Check out picante, phangorn and FD packages if you are exploring community trait structure in a tropical forest
Hey Rachakonda,
Thanks for your suggestion. I am looking for suitable package of R software for null model analysis to identify functional trait-based community assembly pattern. So far I know, picante and phangorn are suitable for phylogenetic analysis.
Picante can be used to generate random communities for your plots.
Moreover, any measure of phylogenetic community structure (Eg. PD, MPD, MNTD) can be used with a functional dendrogram (Pavoine and Bonsall 2011) - http://dbdgs.org/sites/default/files/Pavoine%26Bonsail2011.pdf.
If you are planning to do trait-wise analysis than I would recommend Katabuchi et al. (2012) - http://ctfs.arnarb.harvard.edu/Public/pdfs/Katabuchi%20et%20al%202012%20JEcol.pdf. Methods and analysis are explained in great detail.
So far I know,the Vegan package of R can do the null model, but i don't know how to interpret,and is there any R code to finish it ?
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