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Quite a simple question, looking to see if anybody has experience using both. I have no knowledge of PRIMER, but wondering if R (currently) has the same capacity for data analysis specifically for ecological data using things like perMANOVAs and NMDS plotting.

I know it can be done in R (what can't!?) but I'm more concerned if it's a much longer route to the same conclusion.

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Yes. I have no experience using PRIMER because I didn't want to pay for it, but I have used the vegan package in R extensively for cluster analysis, NMDS, perMANOVA, CCA and PCA. To give you some idea of what R is able to achieve (at least graphically) using this package, I've included a final image from my thesis (first image) and and alternative version I was playing around with that incorporated ggplot2 (second image but not finalized, I did this one differently and wrong in the early days!). As always with R, there is a load of flexibility that I think may be a bit more limited in PRIMER (just a guess). (Also please see my comment - slightly off topic so hence not part of the answer)

enter image description here enter image description here

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  • $\begingroup$ (As far as being a long route to doing it, I think it can be if you're doing it by yourself. I was lucky enough to take a class that involved R how-to documents for each type of analysis. I would be happy to share these with you privately if I could figure out how(?), but I cannot post them since I did not write them and haven't asked permission. $\endgroup$ – HFBrowning Apr 17 '14 at 21:45
  • $\begingroup$ This is great, I'm very glad that those plots can be made and look like that! I would love to look at those, but I really don't know how to coordinate that transfer. $\endgroup$ – smccain Apr 17 '14 at 21:58
  • $\begingroup$ Hey! any chance I could still grab those? I couldn't figure out a way to coordinate the transfer then, but I just made a github. Would it be possible over that? @HFBrowning $\endgroup$ – smccain Jun 5 '14 at 19:20
  • $\begingroup$ It might be - I'll check it out later today. As always, you're also welcome to email me at the address on my profile and I can send them along that way. $\endgroup$ – HFBrowning Jun 5 '14 at 19:37
  • $\begingroup$ I think maybe your email is on private? I couldn't find it when I checked, and still cant! Maybe I'm missing something - sorry! $\endgroup$ – smccain Jun 5 '14 at 19:40

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