[R-sig-eco] rarefied data output

[cristabel.duran]

Hi Stephen,
I attach the results of the rarefaction I did.
It could be great if you can help me with that.

I took a look of other programs like PAST and I also do not find the 
rarefied richness for the plots I used.

Thanks in advance!
Cristabel.


On 03/28/2012 03:12 PM, Stephen Sefick wrote:
> 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.
>>
>>
>>
>> _______________________________________________
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>> R-sig-ecology at r-project.org
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>
> -- 
> Stephen Sefick
> **************************************************
> Auburn University
> Biological Sciences
> 331 Funchess Hall
> Auburn, Alabama
> 36849
> **************************************************
> sas0025 at auburn.edu
> http://www.auburn.edu/~sas0025
> **************************************************
>
> Let's not spend our time and resources thinking about things that are 
> so little or so large that all they really do for us is puff us up and 
> make us feel like gods.  We are mammals, and have not exhausted the 
> annoying little problems of being mammals.
>
>                                -K. Mullis
>
> "A big computer, a complex algorithm and a long time does not equal 
> science."
>
>                              -Robert Gentleman
>
>


-- 
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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