Thanks to everyone who weighed in on my question about community analysis software. All the responses are pasted below. There were lots of votes for R (with the Vegan package), and for PC-ORD. It seems that for quick results and ease of use, PC-ORD is better, while R takes time to learn, but can be used for almost anything.
By the way, one person suggested Ginkgo (which I'd never heard of), which is part of a group of vegetation analysis programs called "VegAna". It's available for free from a research group in Spain, and it runs in Java, so it works on both Mac and PC. It is a quick download, and has a menu driven GUI and looks like it will produce results quickly. Others suggested: Primer, PAST, CAP, FATHOM (for MATLAB). I think the best way to go is, as one person put it: "to compromise time and funds if you can: Purchase PC Ord, get your work done now (and support ecology professor, not computer programmer), and start learning R assuming to shift towards it as your statistical needs and familiarity grows." Thanks again, Joe ===================================================================== I've used both PC-ORD and R for various community analyses. I think Canoco is kind of obsolete. I find PC-ORD very easy to use, and pretty versatile. The options are pretty flexible. Also, the manual is pretty good. I also very highly recommend McCune and Grace's Analysis of Ecological Communities book. In R, of course, you can theoretically do anything you could possibly dream of, but it's a lot of work to learn, and the documentation is spotty (since it's basically written by various volunteers). So it can be tough to figure out what the functions are actually doing, or how to get all the results out, etc. I'd say it's definitely worth learning, but it may take some doing. If you just want to get most of your standard analyses done, I'd go with PC-ORD. You can let me know if you have more specific questions. Good luck! ----------------------------------------------------------------------- I haven't used anything else, so this recommendation might not carry much weight, but I'm a big fan of PC-ORD. It's highlight is automating the nonparametric iterative analysis (Nonmetric Multidimensional Scaling Ordination, MRPP to compare between groups, cluster analysis, indicator species analysis - those are just the tools I've used), but it also includes the more traditional tools like Detrended Correspondence Analysis, TWINSPAN, etc. There is no programming required, and use is pretty intuitive with dropdown menus (and the help files are excellent). Graphics are publication-worthy. The McCune and Grace text (Analysis of Ecological Communities) goes into great detail on all the mathematical details behind each analysis technique, but fortunately one doesn't have to understand all of that because they sum up with recommendations appropriate to community analysis and give examples that spell out how to implement the technique in PC-ORD. I'd say the only tricky thing is setting up your dataset, but that's a piece of cake once you're familiar with the structure required. Users of PC-ORD are also set up to go right into using the relatively new HyperNiche, also put out by MJM software, as the interface is very much the same. HyperNiche is good for regression, including all the traditional regressions as well as Nonparametric Multiplicative Regression, which basically allows one to define species niche-space in terms of environmental variables, to evaluate areas of optimums for your response variable given a whole suite of predictors. (I used it to estimate tree ring age counts from various predictors and was convinced that it was a much more appropriate method that MLR, even though my dataset did conform to the MLR assumptions.) ----------------------------------------------------------------------- I use R and sepecifically the 'vegan' package (short for vegetation analysis), it does most of what PC-ORD does. Also the authors of the vegan package have prepared a really nice user manual/tutorial. ----------------------------------------------------------------------- I expect this is similar to many of the responses you're receiving but I think it comes down to how much delay you can afford before producing your results and whether you'd rather invest time or money. R, which I'm currently teaching myself, does have a bit of a learning curve but has near-comprehensive capabilities and is growing rapidly into the statistics tool that can do anything. It will expand your horizons considerably and is pretty easy to pick up if you're already familiar with something like Matlab. On the flip size, I've been using PC Ord for a few years and been very pleased with its capabilities and ease of use. One draw back is that I don't believe it does Discriminant Analysis (I believe this is true for the newest version as well). However, it gets top marks for tech support as I once reported a bug in the software, corresponded directly with the author received a patch within two days. My recommendation would be to compromise time and funds if you can: Purchase PC Ord, get your work done now (and support ecology professor, not computer programmer), and start learning R assuming to shift towards it as your statistical needs and familiarity grows. ----------------------------------------------------------------------- I have used PC-Ord, CANOCO, and R extensively, although R for non-ordination analyses. I would say without hesitation that PC- ORD is the most user friendly and has the shallowest learning curve. It also has a very nice assortment of ordination alternatives and would be the obvious choice for teaching. On the downside, PC-ORD requires a funky data setup that is a pain to continually monkey with (unusual format in Excel and then use Save As to convert to a .WK1 file). I'm not sure if this formatting issue has changed in newer versions. I've found CANOCO to have greater flexibility and options for advanced analyses, e.g. principal response curves, redundancy analysis, and many others. CANOCO has traditionally been very difficult for graphing the output (but PC-ORD is excellent at this). While I haven't used R for ordination, this software requires a fairly advanced knowledge of command line programming and even though there is a graphical user interface, it wouldn't be easy for students. There is a lot of available support literature for R and there are many, many contributed packages that make the command-line stuff easier. It's of course also free. Ultimately, because I view CANOCO and PC-ORD as complementary packages and am glad I don't own just one. I'd probably recommend PC- ORD for someone just starting out. All of the multivariate analyses I've published, however, have been done with CANOCO. ----------------------------------------------------------------------- The learning curve for R is pretty steep, but in the end it will give you a lot more flexibility (and it's free!). It could be weeks to months before you get your results though, if you take the time to learn it. On the other hand, if you want to do your analyses right now, PC-ORD is very accessible and you'd be getting results pretty much right away. It has most basic community/ordination analyses built in with a menu format. I would look into what analyses you'd like to do and see if they're available in PC-ORD. If you decide to go that way, I also recommend the book Analysis of Ecological Communities by McCune and Grace (developers of PC-ORD). (I did my dissertation analyses in PC-ORD and I liked it a lot but I did run into a few issues as far as flexibility goes. Now I'm trying to learn R and it's rough unless you're used to programming, but I can definitely see the benefits. Once you figure it out, you can ask pretty much any question of your data that you want.) ----------------------------------------------------------------------- I have found CAP to be very easy to use (relatively of course) And it is free!!! Go to the web site of either the paper or the one in the user notes to get the program ----------------------------------------------------------------------- I have experience using PC-Ord and R (but not Brodgar). You do not have to know R or anything like R (e.g. S Plus, SAS, etc) to use PC-Ord. It is a pretty good program with a nice graphical user interface, good help files, and the learning curve is not steep at all. I think that Brodgar puts a graphical user interface on R (so that you don't have to do anymore command line stuff), but I am not familiar with the types of analyses that they offer. PC-Ord has a lot of different analyses (and you probably can't go wrong with it if you are interested in a package with a nice GUI), but certainly not all that one might need as a community ecologist, which is why I reluctantly made the switch to R a couple of years ago. ----------------------------------------------------------------------- You're hearing about some of the point and click programs, just thought I'd alert you to David Jones' FATHOM code for Matlab -- http://www.rsmas.miami.edu/personal/djones/matlab/matlab.html Tons of great stuff there, but you need to know how to use Matlab minimally (copy in data, call the files, etc.). ----------------------------------------------------------------------- I second the plug for R. It does take a while to get comfortable w/ it but, once you do, sky's the limit. The vegan package is great and has decent documentation (see attached). ----------------------------------------------------------------------- You might consider PAST. It is free and Windows-based. Here is a link to the download page: http://folk.uio.no/ohammer/past/ You can find documentation discussing PAST capabilities there. It is easy to download and use. ----------------------------------------------------------------------- R, on its own (well with a text editor to write the scripts; Emacs + ESS is my personal preference) and the vegan package, plus various packages in the Environmetrics Task View: http://cran.r-project.org/web/views/Environmetrics.html would be my choice for what you describe. A further advantage is that new analysis techniques are being written in, or are already available in (or can be easily ported to) R. Of course, R has a fairly steep learning curve. I'd advise you to try to find an introductory course near to you so you can learn to use R. Not because you can't do it on your own (I did as a PhD student 8 years ago), but because unless you have the time to set aside to go through some of the introductory materials and manuals, you're likely to find R frustrating if you jump straight in and try to do some analysis for a job that needs to be done. At least on a course, you are there to learn... One of the advantages of Canoco over competing packages (IMHO, and also based on experiences from several years ago - things may have changed in the intervening period) was the availability of comprehensive support for restricted permutations that allow complex, designed experiments to be analysed via appropriate permutations tests; random shuffling is often not suitable due to spatial/temporal autocorrelation, or blocks/split plots etc. This latter point applies to vegan as well of course, but we are getting closer to the permutation functionality available in Canoco. ----------------------------------------------------------------------- pc-ord is very easy to learn (especially if you get the book _Analysis of Ecological Communities_ by Bruce McCune, James B. Grace, and Dean L. Urban.. does an excellent job of describing the many types of analyses, the pros & cons, and how to do them). you won't need to learn a whole new language as with R. and it is much less expensive than CANOCO. however, CANOCO (and I think R?? not sure) give you more flexibility. pc-ord is more of a "set up the matrices and push the button" kind of a program... CANOCO give much more user control. for example, with CANOCO you can do all kinds of interesting step-wise CCA analyses, but with pc-ord you can only do one type of CCA, with little user control. on the other hand, CANOCO does not do NMS (at least not the program i used a few years ago), which is the analyses that McCune & Grace push as most robust (some do not agree). if i were just starting out, i would go with PC-ord; then pursue R or CANOCO later if I really got into it. Unless you are doing marine community analysis, in which case I think most folks use PRIMER... at least they used to. ----------------------------------------------------------------------- I haven't used either of the programs you listed, but Primer-e is a popular community ecology software package (fairly inexpensive too). http://www.primer-e.com/ ----------------------------------------------------------------------- I've used PC-ORD for years and like it a lot for community analyses. ----------------------------------------------------------------------- Let me just start by saying that I'm not very familiar with any of the software packages out there. And this might be a diversion from your main question.... but we had a need for NMDS recently, and I used Ginkgo. It is a slick, Java-based program that does many multivariate tricks (http://biodiver.bio.ub.es/ginkgo/Ginkgo.htm). It seems fast and might have some neat tricks up its sleeve. ----------------------------------------------------------------------- I think you'll find that R is probably the most efficient route to go, even with the learning curve involved. I still work outside of R to organize and edit data (e.g. SAS and textfiles), but once you have your datasets organized, running analyses are extremely easy in R and there are excellent support networks for getting advice/instruction on running the different packages. The main one used for ordination/mulitvariate analyses is the package VEGAN. And best of all, R is free! ----------------------------------------------------------------------- I have used PC-ORD for years, and also have used PRIMER, which many folks like for these types of analyses (I'm assuming you are after things like ordination and clustering and other "distance-based" approaches to comparing community composition between samples). In many respects, they do the same things, although PC-ORD does more. I have not used CANOCO, but PC-ORD does most of the same things in a much more streamlined fashion. The book written by McCune and Jim Grace that they sell along with PC-ORD is also highly recommended as an intro to all of this stuff. I don't use R currently, so I can't speak to it. The interface in PC-ORD is a bit old-school, so you need to get used to using LOTUS-formatted files, but once you get past that the program works quite simply and it works well in the Windows environment. PRIMER works well with regular old XCEL files without hiccups, which can be nice, but it does less stuff. I tend to use PC-ORD a lot more than PRIMER partly because the underlying analyses are derived from a variety of published sources and are more transparent, whereas the developers of PRIMER wrote and published new analogous versions of many of the analyses (for example, PC-ORD uses multiresponse permutation procedure MRPP and PRIMER uses ANOSIM...both are ways of testing whether groups of samples have significantly different community structure, but ANOSIM is specific to PRIMER whereas MRPP is broadly used in many stats packages and books). I do a lot of this kind of work (mostly with bacterial communities) so if you have other questions about heading down this road I'd be happy to answer them. ----------------------------------------------------------------------- I haven't used either of the programs you listed, but Primer-e is a popular community ecology software package (fairly inexpensive too). http://www.primer-e.com/ ----------------------------------------------------------------------- If you haven't used either Pc-ORd or Canoco I would go with R - it does everything those 2 packages can do and much more that neither can do, plus it is free. Yes the learning curve is a little steeper - but there are plenty of guides that can help you through it. Check out package "Vegan" for ordination. That is what got me into R - I couldn't afford either PC-ord or Canoco, as a grad student or post doc and wanted to do RDA/CCA and more. ----------------------------------------------------------------------- R has a very steep learning curve but if you have time I'd suggest learning R (even though I've never used it for community analysis) just because it is powerful and free. I've never seen Brodgar in action but given that it's an extension for R, it will matter greatly how good their documentation is. You may be able to find free packages for R if you're willing to do a little searching. Documentation on free packages varies from almost nonexistent to really good. PC-Ord (at least the version I have) is pretty picky about how you format your data set but once you get your data into it, it's really easy to use and has pretty good documentation. I think your strategy should depend on how much time you have to devote to a steep learning curve. ----------------------------------------------------------------------- I really enjoy using PC-ORD. The only negative point that I have with the software is getting the data into the correct format to use it. I have used R (although very limited) and for ease of use I would recommend PC-ORD. If you are using direct gradient analysis (known environmental gradients) the software is very useful. Also, if you have no direct gradient then you can use NMS which permutes the data and substitutes artificial data to give the best fits. I am running several analyses in which I have direct gradients and would highly recommend PC-ORD. Another type of software that is available for non-normal data is HYPERNICHE (designed by McCune spp?? also) which deals with nonparametric data.
