[R-sig-phylo] I need help with phylosor...

Marten Winter marten.winter at ufz.de
Tue Feb 17 11:50:08 CET 2009


Heja,

I'm new here, so if this question is totally mad or non-sense, please 
excuse but say at which point :O)

I try to calculate phylo betadiversity somehow. I have a supertree with 
arrtificial branchlengths and I have regional species lists. I'd like to 
use phylosor, which seems to me a good way to measure similarities 
between different phylogenies of the regional species pools.

I', not sure where I made a mistake but I don't get proper results. My 
results are always 2 ??? And I get an error message, which is not 
helpful for me. Could someone please help me?

Thanks in advance!
Marten

AU and BLT are two regions.

str(test2)
num [1:2, 1:3562] 1 0 0 1 0 1 0 1 0 1 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:2] "AU" "BLT"
..$ : chr [1:3562] "Abies_alba" "Abies_balsamea" "Abies_concolor" 
"Abies_fraseri" ...

This is my supertree with artficial branch.length after Grafen.

str(tree.brlen)
List of 5
$ edge : num [1:13392, 1:2] 12206 12207 12208 12209 12210 ...
$ tip.label : chr [1:12205] "Acanthus_balcanicus" "Acanthus_mollis" 
"Acanthus_spinosus" "Hygrophila_polysperma" ...
$ Nnode : int 1188
$ node.label : chr [1:1188] "" "seedplant" "nym2ast" "monocotneudicot" ...
$ edge.length: num [1:13392] 0.013438 0.005572 0.000656 0.156506 
0.001311 ...
- attr(*, "class")= chr "phylo"

(testend<-phylosor(test2, tree.brlen))
Warning message:
In min(phy$edge) : no non-missing arguments to min; returning Inf

AU
BLT 2


-- 

*Marten Winter*

___________________________________________________________________________________________________________________________________

Helmholtz Centre for Environmental Research – UFZ

Department of Community Ecology

Helmholtz-Zentrum für Umweltforschung GmbH - UFZ

Sektion Biozoenoseforschung

Theodor-Lieser-Str. 4
D-06120 Halle (Saale)
Germany

phone: ++49 (0) 345 558-5316 / fax:++49 (0) 345 558-5329

E-mail:_ Marten.Winter at ufz.de___

_http://www.ufz.de/index.php?en=7081_

*DAISIE* - Delivering Alien Invasive Species Inventories for Europe 
_http://www.europe-aliens.org_



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