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Displaying estimators from specpool or estimateR

4 messages · Martin Unterseher, Jari Oksanen

Original
Martin Unterseher
# 
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
Universit?t Greifswald
Institut f?r Botanik und Landschafts?kologie
Lehrstuhl f?r 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
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:
2 days later
Martin Unterseher
# 
Dear Jari,

thank you for your help. The plots are fine and really valuable.
However, when I tried to generate a Sweave-based file, all plot()  
commands following poolaccum() (e.g.

\begin{figure}
<<fig=true>>
pool.data<-poolaccum(data)
plot(pool.data)
@
\end{figure}

resulted in empty or corrupted pdf files. I solved this problem by  
manually saving the poolaccum- plots as pdf and including them in the  
resulting .tex file. Some time-consuming handwork, but ok. So there is  
no urgent need for response.

Best wishes
Martin
On 19 Jan 2011, at 08:58, Jari Oksanen wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
__________

Dr. Martin Unterseher
Universit?t Greifswald
Institut f?r Botanik und Landschafts?kologie
Lehrstuhl f?r 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

  
  


  


      

    

    

      
      

        


  

        

      Jari Oksanen
    

    

      
      #
    

  


  

      
On 21/01/11 15:32 PM, "Martin Unterseher"

        
<martin.unterseher at uni-greifswald.de> wrote:

        

            

      
      
      
    

        
Martin,

This is a quick guess: I haven't checked this. However, I think you should
set

\begin{figure}
<<fig=true,echo=false>>=
...
@
\end{figure}

If you create the fig within latex figure environment, you should only have
the figure, but now you also echo the commands in the same environment.

Cheers, Jari