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

[Sarah Goslee]

I am very sorry, François - I did not follow the link that was
included in my reply, and did not realize it was an illegal copy. As
an author myself, I'm very aware of intellectual property and piracy
issues, and would never knowingly do such a thing. (Though I note that
you just sent it to the list again in your reply - remembering to
delete illegal links is difficult.)

The default inclusion of links in email replies is something I haven't
paid much attention to; I will try to do so in the future.

Meanwhile, as a R-sig-ecology list owner, let me see whether I can do
something to eliminate the link without deleting the whole discussion.



On Wed, Jul 24, 2013 at 9:16 AM, François Gillet
<francois.gillet at univ-fcomte.fr> wrote:
> 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
> Université de Franche-Comté - CNRS
> UMR 6249 Chrono-environnement
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> http://chrono-environnement.univ-fcomte.fr/spip.php?article530
> Phone: +33 (0)3 81 66 62 81
> iPhone: +33 (0)7 88 37 07 76
> Location: La Bouloie, Bât. Propédeutique, -114L
> -------------------------------------------------------------------------------
> Editor of Plant Ecology and Evolution
> http://www.plecevo.eu
> -------------------------------------------------------------------------------
>
>
> 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:
>> > XXXXX (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.functionaldiversity.org