[R-sig-eco] rarefied data output

[Jari Oksanen]

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