I'm doing an inventory of vascular plants in a piedmont gorge (USA) and I'm going to do some transects for community comparisons and analysis. I'll compare communities on different facing slopes and of different elevations. I hear R is the go-to program but are there any other tools I should consider?
For comparing species diversity you can use Estimate S and by using PC-ORD software you can compare many variables at a time and can generate dendrograms
If you collect samples on census areas and evaluate species proportion within the samples somehow, CANOCO 5 should be usefull:
www.canoco5.com
I prefer to use PC-ORD for such questions, but have seen the power of R and would also consider it a good source for community analysis.
Yes, R has very powerful tools that will allow you perform multivariate analyses, biodiversity analyses, etc. There are several packages that will help you to answer these types of questions, for instance, vegan and labdsv have many functions for common community-level analyses, indicspecies for analyses of indicator species, vegetarian for diversity analyses, iNEXT for rarefaction, etc...I guess it'll depend on your research questions and hypothesis that you can choose what types of analyses you can carry out. Beware that R is not very friendly, you need to know about programming and the learning curve is somewhat steep; however, if you learn R language, you can perform pretty much anything you wish. You move away from windows-based software where you click, click and get an output but you'll have absolute control of what you are doing. I suggest you to read Brocard et al. 2011. Numercial Ecology with R. Springer, for an excellent introduction about R and multivariate analyses.
I agree that R is a very diverse tool and can be used for free, which is certainly a bonus, but be aware that the learning curve for R is steep and the enormity of its capabilities can be overwhelming. Once you know R it is brilliant. A good package for community work is PRIMER 6 (plus Permanova). This you would have to pay for once, but it is far more intuitive and specifically designed for the multivariate analyses you will need. Citing its use may also be easier. If cost is not your issue I would use Primer, I have used both for plant communities of NSW Australia
I should add that R-Studio is far more user friendly if you wind up going down the path of using R.
I have done several community analyses using the vegan package in R. Using the adonis function/command (which will run a perMANOVA; Anderson 2001) is a great place to start. I have used PC-ord and Primer and I don't think they're any easier to learn than R. If you have any questions about how to run it, let me know.
I would also agree that R is incredibly powerful, albeit with a steep learning curve. There is a great book by Gregg Hartvigsen - "A Primer in Biological Data Analysis and Visualization Using R". He also introduces you to R Studio. PC-ORD is also good. Also, depending on what specific tests you are looking to perform I have found PASSAGE to be useful and fairly user friendly (at least for my work).
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