[R-sig-eco] doubt in generating loops with For

[Vít Syrovátka]

Hi Thiago,
I am not familiar with the diversity measure you are trying to calculate 
and your example code is not complete - one can not simulate your comm 
and dist objects.
But at the first sight one can see that in your loop you are trying to 
select columns 1, 2, 3,... 1000 from the comm matrix, which probably has 
only 10 columns (if sites are in columns and species in rows, contrary 
to how such data are traditionally stored).

for(z in 1:10)
instead of
for(z in 1:1000)
should do the job.

Vit

Dne 2015-04-15 23:24, Thiago A. Pires napsal:
> Hi guys,
> 
> I have a question when trying to generate 1000 measures with "for"
> function. For example, I have 10 locations with 5 species , and I want 
> to
> apply a diversity measure on each site. But when I try to run one is 
> with
> my function, I can not, I get an error message: "Error in com[, z] :
> subscript out of bounds", and I think it should be a simple mistake, 
> but
> I'm not seeing. If you guys can help with it, I would appreciate. Right
> below is an example for my code:
> 
> comm= a community matrix with 10 sites and 5 species
> dist= a pairwise distance-based matrix of species
> ​
> ​ for (z in 1:1000)
>   {
> 
>   func.sim[z,]<- (t(comm[, z]) %*% (as.matrix(dist)^2) %*%
>                  comm[, z])/2/(sum(comm[, z])^2)​
> 
>   }
> 
> 
> ​Error in comm[, z] : subscript out of bounds​
> 
> 
> 
> 
> 
> 
> ​Best regards,
> 
> Thiago.​
> 
> 
> _____________________________________________________________
> 
> *Thiago A. Pires*
> Ph.D. student in Ecology -  Instituto de Biologia - UNICAMP
> Collaborator Researcher - Laboratório de Ecologia e Sistemática - 
> UNIFESP
> 
> 
> Email: pires.thiagoaugusto at gmail.com / Skype: thiago.augusto.pires
> Home Page:
> http://thiagoaugustopires.wix.com/naturevisions
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