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

[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:

> 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
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

__________

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