[R-sig-eco] Heat Map for species - code from Numerical Ecology with R

[THIOULOUSE JEAN]

Hi François,

Note that Jari and yourself also encourage piracy in the same way ;)

Jean


Le 24 juil. 2013 à 15:16, François Gillet <francois.gillet at univ-fcomte.fr>
 a écrit :

> Valerie and Sarah,
> 
> Thank you for encouraging piracy by posting the URL of an illegal PDF of
> our book :-(
> 
> By the way, just look at ?vegemite and you'll find easily the solution to
> your problem: with the argument scale="log" your numeric data will be
> converted to 1-char symbols.
> 
> François
> 
> -------------------------------------------------------------------------------
> Prof. *François Gillet*
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> 
> 2013/7/24 Sarah Goslee <sarah.goslee at gmail.com>
> 
>> Hi Valerie,
>> 
>> Did the suggestions given on the R-help list fail to work?
>> 
>> You do need to provide you abundance data as one character, as specified in
>> ?vegemite which also gives suggestions for conversion.
>> 
>> Sarah
>> 
>> On Tuesday, July 23, 2013, Valerie Mucciarelli wrote:
>> 
>>> Hello,
>>> 
>>> I am relatively new to R and I am working through the code that is
>>> provided in the book Numerical Ecology with R:
>>> (pg 79)
>>> 
>>> and I have run across an error message that I can't seem to figure out.
>>> 
>>> I am using the vegan, ade4, gclus and cluster packages. The code is as
>>> follows:
>>> 
>>> # Ordered community table
>>> # Species are ordered by their weighted averages on site scores
>>> 
>>> or <- vegemite(spe, spe.chwo)
>>> 
>>> spe is the dataframe, here is part of it:
>>> 
>>>     AGA   ANT  BON   CAL1   CAL   CER   CRY   DES  EUTH FRY
>>> 1  0.420 0.092 0.051 0.000 0.975 0.000 0.111 0.000 0.127 0
>>> 2  0.000 0.000 0.007 0.002 0.915 0.000 0.000 0.000 0.151 0
>>> 4  0.000 0.008 0.000 0.009 0.124 0.003 0.000 0.000 0.095 0
>>> 7  0.000 0.002 0.003 0.002 0.121 0.002 0.000 3.573 0.180 0
>>> 12 0.000 0.020 0.000 0.002 0.444 0.001 0.000 0.000 0.242 0
>>> 13 8.727 0.000 0.000 0.000 0.743 0.000 0.000 0.000 0.050 0
>>> 14 2.163 0.009 0.000 0.003 1.121 0.000 0.000 0.000 0.051 0
>>> 15 0.000 0.004 0.000 0.000 0.109 0.000 0.000 0.000 0.007 0
>>> 18 9.021 0.018 0.002 0.000 0.286 0.000 0.000 0.000 0.028 0
>>> 19 0.000 0.038 0.000 0.019 0.509 0.000 0.000 0.000 0.155 0
>>> 
>>> spe.chwo came from:
>>> 
>>> spe.norm <- decostand(spe, "normalize")
>>> spe.ch <- vegdist(spe.norm, "euc")
>>> spe.ch.UPGMA <- hclust(spe.ch, method = "average")
>>> spe.chwo <- reorder.hclust(spe.ch.UPGMA, spe.ch)
>>> 
>>> 
>>> and the error is:
>>> 
>>> Error in vegemite(spe, spe.chwo) :
>>> Cowardly refusing to use longer than 1 char symbols:
>>> Use scale
>>> 
>>> The data in the dataframe is biomass data recorded to 4 digits. I'm
>>> wondering if this code is not working because my data is more than one
>>> digit long.
>>> 
>>> Any suggestions or insight on how to get this code to work would be
>>> greatly appreciated.
>>> 
>>> Thank you,
>>> 
>>> Val
>>> 
>>> 
>> 
>> --
>> Sarah Goslee
>> http://www.stringpage.com
>> http://www.sarahgoslee.com
>> http://www.functionaldiversity.org
>> 
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>> 
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