[R-sig-eco] Displaying estimators from specpool or estimateR

[Jari Oksanen]

Martin,

I have supposed that functions poolaccum() and estaccumR() do this. If
they are not suitable for your needs, please tell me what you want to
achieve. 

These two functions have been in vegan since release 1.15-4 (7
September, 2009).

Cheers, Jari Oksanen 


On Tue, 2011-01-18 at 09:22 +0100, Martin Unterseher wrote:
> Dear all,
> 
> as far as I know, functions specpool and estimateR (both in package  
> vegan) provide only the final values of the non-parametric estimators.  
> In contrast to that, EstimateS calculates a real curve of each  
> estimator function. To me this is of importance to evaluate the  
> stability and reliability of the final value calculated by the  
> respective estimator.
> 
> Carsten Dormann found a way to achieve this in R and provided this  
> function for me:
> 
>  > reps=100
>  > sequence.abies.myk<-1:nrow(abies.myk.com) #abies.myk.com is my  
> species-samples matrix from mycorrhizal fungi of Abies alba
>  > res.abies.myk<-matrix(ncol=9, nrow=length(sequence.abies.myk))
>  > colnames(res.abies.myk)<-names(est.abies.myk) #est.abies.myk is the  
> result from specpool(abies.myk.com)
>  > for (i in sequence.abies.myk)
> {
>     sample.raw.abies.myk <- replicate(reps,  
> specpool(abies.myk.com[sample(x=1:nrow(abies.myk.com), size=i),]),  
> simplify=TRUE)
>     subsample.abies.myk <- matrix(unlist(sample.raw.abies.myk),  
> nrow=9, ncol=reps)
>     rownames(subsample.abies.myk) <- names(sample.raw.abies.myk)
>     res.abies.myk[i, ] <- rowMeans(subsample.abies.myk)
> }
> 
> It works fine. For small data sets and many replications, curves  
> shapes are in concordance with the EstimateS output. For larger data  
> however, calculations with high values of "reps" would take hours to  
> days. If you use small values for "reps" instead the curves will  
> appear jagged and are often not publishable.
> 
> Does any one know of alternatives to display estimator curves in R?
> 
> Thanks
> Martin
> __________
> 
> Dr. Martin Unterseher
> Universität Greifswald
> Institut für Botanik und Landschaftsökologie
> Lehrstuhl für Allgemeine und Spezielle Botanik
> Grimmer Str. 88
> 17487 Greifswald
> 
> Tel. 03834 / 864184
> Fax. 03834 / 864114
> 
> http://www.botanik.uni-greifswald.de/100.html
> http://dgfm-ev.de/index.php?id=munterseher
> 
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