Gavin and Vìt, thank you very much for you prompt and informative replies, They were very helpful.
Best regards, Jonas From: Vít Syrovátka <syro...@sci.muni.cz> To: Gavin Simpson <ucfa...@gmail.com> Cc: r-sig-ecology@r-project.org Date: 10.08.2013 16:11 Subject: Re: [R-sig-eco] Plotting adonis (vegan) results Sent by: r-sig-ecology-boun...@r-project.org Thank you, Gavin. Yes, I meant the methods you listed, but fully agree that PCoA will be the most reasonable method with respect to what adonis or betadisper are doing. Vit Dne 2013-08-10 15:53, Gavin Simpson napsal: > Just one point Vit, re "...or choose another ordination technique." If > by > that you meant you could use PCA or CA or NMDS etc, then I don't think > that > will be useful. We use PCoA because the inputs to adonis(), > betadisper, etc > are dissimilarity matrices and the aim is to show those > dissimilarities > (and the group centroids/dispersions) as best as possible whilst > preserving > the direct link to the distance values (ie why we don't use NMDS). I > guess > you could use PCA for this if you have Euclidean distances, CA if you > want > Chi-square etc, but not NMDS as it works on ranks so you'd get an odd > representation of what adonis() or betadisper() do. > > As for the rest, you seem to have that right, though the cmdscale() > call > might take a little bit more effort if you want to handle negative > Eigenvalues that arise with some dissimilarity metrics. > > > On 10 August 2013 06:33, Vít Syrovátka <syro...@sci.muni.cz> wrote: > >> Dear Jonas, >> I've just had a look into the paper (Friberg et al (2013)), but there >> is >> no information on what kind of ordination they used (at least it is >> very >> well hidden). Hard to believe, maybe I am wrong, but can't find >> anything >> about that. And they used different ordination techniques to >> visualise the >> groups with regard to the results of 'adonis()' and 'betadisper()' - >> compare Fig.1 and Fig. 2. Maybe that brought the confusion. >> >> The thing is that 'adonis()' tells you, whether the groups >> consistently >> differ in their community composition, and then it's up to you to >> chose an >> ordination technique to visualize the groups. Probably that would be >> an >> ordination that approximates the same distances used in 'adonis()' >> (or >> 'betadisper()'). The plot method of 'betadisper()' uses Principal >> Coordinate Analysis (PCoA), which you can use to visualize the >> results of >> 'adonis()' as well (as Gavin and Jari pointed out) or do it by your >> own or >> choose another ordination technique. >> >> A small example with PCoA: >> >> ## taken from ?betadisper: >> library(vegan) >> data(varespec) >> >> # create the dist object >> dis <- vegdist(varespec) >> >> # create grouping variable; First 16 sites grazed, remaining 8 sites >> ungrazed >> groups <- factor(c(rep(1,16), rep(2,8)), labels = >> c("grazed","ungrazed")) >> >> # Calculate multivariate dispersions >> mod <- betadisper(dis, groups) >> >> # Plot PCoA ordination with differentiated groups = visualize the >> dispersions of groups in 2D ordination space >> plot(mod) >> >> ## now create the same plot on my own (though with different graphic >> parameters) >> # calculate the PCoA ordination sites' scores >> pcoa<- cmdscale(dis) >> # plot them with different symbols for groups >> plot(pcoa, asp=1) >> # and add spiders and hulls >> ordispider(pcoa, groups) >> ordihull(pcoa, groups) >> >> If I am wrong in any point, will be glad if someone corrects me. >> Cheers, >> Vit >> >> >> Dne 2013-08-09 19:25, Gavin Simpson napsal: >> >> What Jari meant was if you use `betadisper()` on your data then it >> will >>> give you an object that has a `plot()` method which will give you >>> something >>> of relevance to what `adonis()` and the whole PERMANOVA method is >>> doing. >>> It >>> plots the groups centroids and dispersions of the groups in >>> principal >>> coordinates space. I don't have easy access to that journal at the >>> minute, >>> but will look when I get back from this conference next week. >>> >>> You can see how `betadisper` and its `plot` method works in the mean >>> time >>> if you want to customise how things are plotted. >>> >>> Gavin >>> >>> On 9 August 2013 06:54, <jonas.pers...@niva.no> wrote: >>> >>> Hi all >>>> >>>> I'd like to plot my results from adonis (vegan). Internet searches >>>> found >>>> me an older post here in which Jari Oksanen wrote: "adonis() does >>>> not >>>> have >>>> plot method, but you can use betadisper for plots." But I'm afraid >>>> I >>>> don't understand how to do it this way. >>>> >>>> How can I a) make a plot of adonis results? b) manipulate the >>>> layout of >>>> adonis/betadispers figures to my liking? >>>> My main inspiration for both adonis and betadispers results >>>> plotting is >>>> Friberg et al (2013) Hydrol. Process. 27, 734?740, so I'd like to >>>> be able >>>> to produce something similar. >>>> >>>> Cheers, >>>> Jonas _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]]
_______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology