R help - Jul 2013 - Heat Map for species - code from Numerical Ecology with R

Hello,   I am relatively new to R and I am working through the code that is
provided in the book Numerical Ecology with R 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 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.  Here is an example of part of the dataframe:
 AGA   ANT   BON  CAL11 0.42 0.092 0.051 0.0002 0.00 0.000 0.007 0.0024 0.00
0.008 0.000 0.0097 0.00 0.002 0.003 0.002

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 with
biomass data would be greatly appreciated. Thank you, Val
	[[alternative HTML version deleted]]

Hi Valerie,

Are you using your own data or data provided by the authors?

If the latter, where can we get it?

If the former, please provide a reproducible example using dput() to
include some of your data.

Also, please resend your message with HTML mail turned off so we can
actually read it.

Providing a reproducible example makes it possible for us to figure
out what went wrong.

Sarah

On Tue, Jul 23, 2013 at 2:49 PM, Valerie Mucciarelli
<soccermucc at hotmail.com> 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 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 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.  Here is an example of part of the dataframe:
>  AGA   ANT   BON  CAL11 0.42 0.092 0.051 0.0002 0.00 0.000 0.007 0.0024
0.00 0.008 0.000 0.0097 0.00 0.002 0.003 0.002
>
> 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 with
biomass data would be greatly appreciated. Thank you, Val
>         [[alternative HTML version deleted]]
>
-- 
Sarah Goslee
http://www.functionaldiversity.org