On Tue, 2011-10-04 at 08:45 +0000, Ashley Houlden wrote: > Hi, <snip /> > #distance matrix of samples using bray curtis > d= bcdist(mydata, rmzero=FALSE)
In addition, you don't necessarily need ecodist for the bray curtis distance. vegdist() in vegan will compute this for you. Not that there is anything wrong with ecodist I hasten to add - just that you can do this all in vegan if you wanted. G > And then using the distance matrix from this to use for adoins? Is this > correct. > > With this I have then run Adonis > > results = adonis(d ~ wood, envdata_fit, permutations = 1000) > > and get significant values to see if sig diff in diversity between wood and > grass habitat. > > However I have been reading about combining the variables, but there seems to > be different ways for example > > results = adonis(d ~ wood+soil, envdata_fit, permutations = 1000) > > so get sig values for Wood and soil > > or > > results = adonis(d ~ wood*soil, envdata_fit, permutations = 1000) > > And I get sig values for wood, soil, and wood soil interaction. > > This seems to make sense, however for both if I put the variable the other > way around (soil+wood or soil*wood) I get very different sig values, even > accounting for the fact they vary slightly due to the permutations. So whats > is going on and why to the the values change so much? > > I was also wondering in Adonis, can you nest treatments, so see effect of > soil removing the effect of woodland as you can with anova? > > Another general questions as well, if I have more than two groups in a > treatment, say for soil, clay, sand, loam and do the stats, and I get a > significant value, what does it actually mean, is it that soil generally has > an effect, with each group separate, or there are general differences between > soils which may be one group is very different to the other two? > > Many many thanks to anyone who can help me as I have asked people who use R > near me and no-one is sure and uses Adonis.. > > Ash > ________________________________ > > No virus found in this message. > Checked by AVG - www.avg.com<http://www.avg.com> > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
