[R-sig-eco] adonis model specification

[Peter Solymos]

Christine,

There is no summary method for adonis. After calling the function,
simply use print:
x <- adonis(...)
x

And you are right, you can supply raw data and use the method argument
in adonis to define dissimilarity index (which is "bray" by default).

Cheers,

Peter

Péter Sólymos
Alberta Biodiversity Monitoring Institute
Department of Biological Sciences
CW 405, Biological Sciences Bldg
University of Alberta
Edmonton, Alberta, T6G 2E9, Canada
Phone: 780.492.8534
email <- paste("solymos", "ualberta.ca", sep = "@")



On Tue, Sep 29, 2009 at 3:47 AM, Christine Griffiths
<Christine.Griffiths at bristol.ac.uk> wrote:
> Dear R helpers,
>
> I have collected species composition data (counts of 24 species)from 16
> plots. I am interested in seeing how different the plots are from each
> other and how this changes over time.
>
> My design is as follows: I repeatedly sampled the plots each month for 11
> months. The plots are grouped into three treatments (1-3), which were
> replicated 6 times (blocks 1-6). I have unbalanced data in that I lost 2
> replicates from 2 of the treatments, so I have only 16 plots in total.
>
>> From what I have read, I want to use the adonis function in the vegan
>
> package. Having had a look at the set up of the dune data example, I have
> set up my data in the same format. Below is an idea of my data.
> I have 16 plots * 11 months = 176 sites. Since in 3 of these there were no
> species, I only have 173 sites.
>
> dataset.plot.env[1:5,]
>  ID Area Treatment Block BlockID Month
> 1  1    1         1     1       1     1
> 2  2    1         1     2       2     1
> 3  3    1         1     3       3     1
> 4  4    2         1     4       4     1
> 5  5    2         1     5       5     1
>
> block<-as.factor(Block)
> month<-as.factor(Month)
> area<-as.factor(Area)
> treatment<-as.factor(Treatment)
>
> ### data is counts. x? are species.
> dataset.plot.count[1:5,1:15]
>  X5 X6 X7 X8 X9 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
> 1 11  2  1  0 58  10  28 137   0   0  87  18  68  10   0
> 2  6 10  2  0 36   1  26 192  65   0   6  35  94  14   0
> 3  2  0  0  0 27  41  33 394  16   0   3  14   4  16   0
> 4 22 54  7  0 26  42  10 275 137   4  22  10  30   1   0
> 5  1  5 10  0  0  19  45 599  60   0   6   3   0   5   0
>
> library(vegan)
> data1<-vegdist(dataset.plot.count,method="morisita")
>
> ## since I am using count data I chose morisita index.
> ## I read that first I needed to convert my data into a dissimilarity
> ## matrix. Or is this not necessary if I stipulate method in the adonis
> ## function?
>
> m1<-adonis(data1~treatment,data=dataset.plot.env,permutation=200,method="mo
> risita")
> summary(m1)
>
> If I do either of the above or the following, I get this result.
> m1<-adonis(dataset.plot.count~treatment,data=dataset.plot.env,permutation=2
> 00,method="morisita")
> summary(m1)
>
>            Length Class      Mode
> aov.tab        6    data.frame list
> call           4    -none-     call
> coefficients   0    -none-     NULL
> coef.sites   519    -none-     numeric
> f.perms      200    -none-     numeric
> model.matrix 519    -none-     numeric
> terms          3    terms      call
>>
>
> I am unsure exactly of what I am doing wrong or what I need to specify. I
> would be grateful for any help and guidance.
>
> I have read that I can use strata to specify a time series. If so would I
> code it like this:
> m1<-adonis(dataset.plot.count~treatment,data=dataset.plot.env,strata=datase
> t.plot.env[,"Month"],permutation=200,method="morisita")
> ## This doesn't work either though.
>
> I had originally planned on doing MRPP but having read that it is less
> robust I opted for adonis. With MRPP, I was going to test the difference in
> species composition between treatments at each month as I think I am unable
> to test this for the whole study. Using adonis, do I need to do a number of
> tests or can I simply run the following?
>
> m1<-adonis(dataset.plot.count~treatment*month*block,data=dataset.plot.env,s
> trata=dataset.plot.env[,"Month"],permutation=200,method="morisita")
>
> I have had a look at Oksanen 2009, Multivariate Analysis of Ecological
> Communities in R: vegan tutorial. I have not been able to find much more
> information on adonis. Could anyone direct me to more literature please.
>
> Any help would be much appreciated.
>
> many thanks
> Christine
>
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