[R-sig-eco] Heat Map for species - code from Numerical Ecology with R
Gavin Simpson
gavin.simpson at ucl.ac.uk
Thu Jul 25 04:49:59 CEST 2013
Charles,
You are way off base here. The list is not hear to promote the violating
of copyright. Your email *is* incredibly disrespectful. Are you paying
Francois to teach you? No! So what the hell does his profession have to
do with your or anyone's right to rip off his hard work?
I suspect Francois reported (if he did - I have no evidence either way)
it so Springer could do something about the source (i.e. the site) not
to try to get anyone into trouble.
I don't see anything "lordly" about the reply - it was a two-line
comment pointing out the issue, though somewhat misguided at Sarah as I
can fully understand not noticing a link or certainly not following it
to ascertain its legality.
Quite frankly your email and tone are not welcome here.
Gavin
(An Open Access advocate, before you ask!)
On Wed, 2013-07-24 at 16:00 +0200, Charles Novaes de Santana wrote:
> Dear Franois,
>
> Sorry if this message seems to be disrespectful. But it would be unfair if
> I let you do what you are doing to these two researchers without saying
> anything.
>
> Did you really need to send an email to Springer "ethics.reporting"? And
> did you really need to answer their question so lordly? You look like a kid
> that cries for "Mom"! As a Professor, you are supposed to teach and to
> encourage everyone to make the right thing. You are not supposed to
> "punish" anybody!
>
> We are members of a discussion list with the mission of sharing knowledge.
> The mission of helping people with their questions and to make science
> evolve with new and motivated scientists! More than that: It is a list
> about R, that is a free software, which major principle is "Free
> Knowledge". Further, isn't "share the knowledge" one of the missions of a
> Professor, too? Your EGO can not be higher than all of these!
>
> Just to finish: It looks like you have never downloaded any paper, software
> or document from internet without the allowance of the "right owners".
> Everybody knows it is not true! Look at your own message, as Jean smartly
> suggested!
>
> If we can not share knowledge in this list, I think it is time to go away!
> So, good bye, enjoy the knowledge you think is yours!
>
> Charles
>
> On Wed, Jul 24, 2013 at 3:16 PM, Franois 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.
> >
> > Franois
> >
> >
> > -------------------------------------------------------------------------------
> > Prof. *Franois Gillet*
> > Universit de Franche-Comt - CNRS
> > UMR 6249 Chrono-environnement
> > UFR Sciences et Techniques
> > 16, Route de Gray
> > F-25030 Besanon cedex
> > France
> > http://chrono-environnement.univ-fcomte.fr/
> > 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, Bt. Propdeutique, *-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:
> > > > http://xa.yimg.com/kq/groups/19243105/1919134110/name/Numerical.pdf(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
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
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> > >
> >
> > [[alternative HTML version deleted]]
> >
> >
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> >
> >
>
>
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--
Gavin Simpson, PhD [t] +1 306 337 8863
Adjunct Professor, Department of Biology [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
523 Research and Innovation Centre [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada
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