rarefied data output

I don't know the answer to you question, but if you had used dput to 
make a copy and pasteable example (with data) then I will take a look 
and see if I can't figure it out.
good luck,

Stephen

On Wed 28 Mar 2012 04:58:33 AM CDT, cristabel.duran wrote:

Dear list,

I have a species matrix with species abundances (spp) and in other
matrix with environmental information (env) with several factors. The
factor I am interested in (mhab5) has five levels.
The spp matrix looks like that:

      Aba_sp Alc_gla Ann Ann_1uc Apo Asp_dec Asp_sp Bur Bur_1 Bur_1uc 
Bur_2
P1       0       0   0       0   0       0      0   0     0       
0     0
P2       0       0   0       0   0       0      0   0     0       
0     0
P3       0       0   0       0   0       0      0   1     1       
0     0
P4       0       0   0       0   0       0      0   0     0       
0     0
P5       0       0   0       0   0       0      0   1     0       
0     2
P6       0       0   0       0   0       0      0   0     0       
0     0
P7       0       0   0       0   1       0      0   0     0       
0     0


Beside of testing for differences in species richness between the levels
of the factor mhab5, I want to use the rarefied data for a model. In
other words I need the rarefy richness for P1, P2, P3, and so on.....

I used the function accumcomp (BiodiversityR) which internally uses the
function rarefy (vegan)
acumhab5<- accumcomp(x=spp, y=env, factor="mhab5",
method="rarefaction", conditioned=TRUE, legend=T)

I am able to extract the rarefied species richness with
richnessmhab5<- t(acumhab5[ ,  , 2])

I get this output:

      mhab5
obs    Border Branches     Crown    Trunk  Undist.
    1  15.66701 11.88617  8.582444 19.37374 16.85696
    2  23.31066 18.17601 13.536749 27.53000 23.01568
    3  28.83948 22.61587 17.677169 33.35105 26.53217
    4  32.98145 26.06969 20.730801 37.93189 29.04925
    5  36.39266 28.90257 23.480157 41.76465 30.97731
    6  39.39713 31.30142 25.594925 45.01781 32.62629
    7  41.92287 33.47224 27.560948 47.98189 34.00000


With this output I am not able to know which results correspond to which
plot (see in spp matrix: P1, P2, P3, etc)
any clue how can I get the information in the order I need?

have a nice day,
Thank you very much!
Cristabel.

-- 
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**************************************************
sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
**************************************************

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