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
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