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.
Fran?ois
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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