[phylocom-user] Comtrait

Ken Whitney kwhitney at rice.edu
Sun Dec 13 11:44:47 PST 2009


We are having the same Comtrait issue as Masatoshi: the "rankLow" and 
"rankHigh" output don't seem to make sense.  Also, there seems to be an 
error in estimating MeanRndMetric for certain samples, but which samples 
are problematic varies across different runs of the same files.

Pasted below is the beginning of the output generated by Comtrait (using 
all default settings).  The traits and sample input files were saved as 
tab-delimited text in Excel, the .txt was deleted, files then checked in 
Notepad++.  The files can be obtained here:

http://www.ruf.rice.edu/~kwhitney/links.htm


Many thanks for any help,
Ken


Trait 	Sample 	NTaxa 	Mean 	Metric 	MeanRndMetric 	SDRndMetric 
SESMetric 	rankLow 	rankHigh 	runs
HAG 	A1 	17 	18.49412 	171.7206 	1.#INF00 	-1.#IND00 	-1.#IND00 
4063654 	4064561 	999
HAG 	A2 	22 	21.20909 	131.4866 	1.#INF00 	-1.#IND00 	-1.#IND00 
1600220272 	1768778071 	999
HAG 	A3 	15 	27.15333 	137.3155 	442.6903 	194.681 	-1.56859 
1969843833 	1852795718 	999
HAG 	A4 	18 	26.31667 	92.01323 	437.6531 	174.2375 	-1.98373 
1952541797 	1225340144 	999
HAG 	A5 	7 	26.3 	82.17333 	434.2096 	286.9327 	-1.2269 	174680479 
1969712401 	999
HAG 	A6 	7 	25.14286 	33.45286 	441.8287 	292.992 	-1.39381 	822687049 
1953461832 	999


Trait    Sample    NTaxa    Mean    Metric    MeanRndMetric    
SDRndMetric    SESMetric    rankLow    rankHigh    runs
HAG    A1    17    18.494118    171.720596    1.#INF00    -1.#IND00    
-1.#IND00    4063654    4064561    999
HAG    A2    22    21.209091    131.486588    1.#INF00    -1.#IND00    
-1.#IND00    1600220272    1768778071    999
HAG    A3    15    27.153334    137.315521    442.690338    
194.680954    -1.568591    1969843833    1852795718    999
HAG    A4    18    26.316666    92.013229    437.653107    174.237503    
-1.983728    1952541797    1225340144    999
HAG    A5    7    26.299999    82.173325    434.209625    286.932709    
-1.226895    174680479    1969712401    999
HAG    A6    7    25.142857    33.452858    441.828705    292.992035    
-1.393812    822687049    1953461832    999

------------------
Ken Whitney
Assistant Professor
Dept. of Ecology and Evolutionary Biology
Rice University
Houston, TX 77005 USA
713 348 3057
http://www.ruf.rice.edu/~kwhitney/



phylocom-user-request at lists.phylodiversity.net wrote:
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>    1. Comtrait (Masatoshi KATABUCHI)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Nov 2009 20:32:01 +0900
> From: Masatoshi KATABUCHI <mattocci27 at gmail.com>
> To: phylocom-user <phylocom-user at lists.phylodiversity.net>
> Subject: [phylocom-user] Comtrait
> Message-ID:
> 	<1e31af440911300332k653e44cfgbe9587e0747f4631 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I am having trouble using Comtrait.
> Comstruct produces good output files, but when I run Comtrait, I get odd
> output files that have very large "rankLow" and "rankHigh" values
> irrespective of randomization number.
>
> I would appreciate it if anyone could give me some advice on this.
>
> Best regards,
>
> Masatoshi Katabuchi
>
>   
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