On 03/28/2012 05:36 PM, Jari Oksanen wrote:
> On 28 Mar 2012, at 12:59, 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?
> Cristabel,
>
> I am not quite sure what you try to get. However, you used function that gives you the richness of *accumulated* plots (=several plots combined together). There is no way of knowing the rarefied richness of single plots if you ask for accumulated results. Now I really don't know what you want to get, but here two alternatives:
> - if you want to know the rarefied richness of single plots, use rarefy().
> - if you want to know which plots belong to which mhab5 data, look at your data.
>
> Cheers, Jari Oksanen
Dear Jari,

thank you for your help. I want to know the rarefied richness of single 
plots.
and I  just now rarefied my data within each factor level with rarefy(), 
and I got what I was looking for.

I was wondering that the rarefy richness really is much lower than the 
original:
original:

  P1  P5  P9 P11 P17 P23 P30 P33 P36 P38 P41 P50 P54 P56 P59 P62
   9  14   2   8  10  11   6   7   6  16  13  10  11  12  10  12


rarefied:

       P1       P5       P9      P11      P17      P23      P30      P33      P36
3.313725 2.827956 2.000000 3.293040 2.946823 3.592810 2.263004 3.087552 3.195238
      P38      P41      P50      P54      P56      P59      P62
3.659412 3.547713 2.555684 3.376906 3.202633 3.227595 3.428148


My data is from regeneration of tropical forest, with few species with 
high abundance and lots of species with few abundance.

I do doubt of the results, but as I never worked with rarefaction I do 
not know how interpret such a disparity between non-rarefied and 
rarefied richness.

Thank you very much,
Cristabel.


-- 

Dr. Cristabel Durán Rangel.
Institute of Silviculture. Faculty of Forest and
Environmental Sciences. University of Freiburg.
Germany
Telf: +49 (761) 203 8603 (ofc)
https://portal.uni-freiburg.de/waldbau

"Man lernt die Physiognomie einer Landschaft desto besser
kennen, je genauer man die einzelnen Züge auffaßt, sie
untereinander vergleicht und so auf dem Wege der Analysis
den Quellen der Genüsse nachgeht, die uns das große
Naturgemälde bietet."
                 Alexander von Humboldt, 1799


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