On Fri, 2012-12-14 at 06:22 -0600, Stephen Sefick wrote:
> >>> a) Which ordination method would be better for my data : PCA knowing
> >>> that the represented inertia is 35.62% or NMDS with a stress value about
> >>> 0.22?
> >>>
> >> My opinion is PCA on hellinger transformed relative proportions
gesdd-tp7556369p7577802.html
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [
les)
>
> CCA1CCA2CCA3CCA4 CA1 CA2
> Vit1 -0.1424 -0.4923 -1.7924 -0.2924 -0.72976 0.08807
> Vit2 -0.1424 -0.4923 -1.7924 -0.2924 0.66991 -0.08085
> .
> .
> .
>
> Biplot scores for constraining variables
>
>CCA1CCA2
rg.ru
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On Mon, 2013-02-25 at 13:18 -0500, Sarah Loboda wrote:
> Hi,
> I have trouble to obtain the ordination graph I want. I want to have 4 RDA
> biplot on the same page and I don't want to have (or I want to modify) the
> axis numbers. I want the marks on the axis without numbers to maximize the
> space
On Thu, 2013-03-07 at 10:48 -0400, carolina monmany wrote:
> Hi all,
>
>
> I would like to use ordipointlabel() to plot a RDA but the function
> only displays species and sites. How can I include environmental
> variables as vectors?
>
>
> Thanks!
You can use
text(ord, display = "bp")
(where
On Thu, 2013-03-07 at 15:37 +, Mark Fulton wrote:
> There's probably something "off the shelf", but
> I use a little function written in R:
>
> #A function for doing an xyz bubbleplot.
> bubbleplot <- function(x, y, z, bmax=4, bmin=.5) {
> plot(x,y, type="n")
> z <- z-min(z); z <- z/max(z)
On Thu, 2013-03-07 at 11:13 -0800, Rich Shepard wrote:
> On Thu, 7 Mar 2013, Philippi, Tom wrote:
>
> > I would look at packages bio.infer, paltran, fossil, and analogue, and
> > search to see if anyone has pushed them in the direction you want to go.
To this list I would add Steve Juggins' excel
On Thu, 2013-03-07 at 10:59 -0800, Philippi, Tom wrote:
> Jay--
>
> I'm not sure how one would combine SEM / graphical models with
> compositional dissimilarity as a response. You might be able to fit a
> series of models in adonis() or capscale(), comparing just direct factors
> to direct + inte
nswer this question
> and (this not being my subject specialty) I'm at a bit of a loss.
>
> If there are relevant R packages/vignettes/manuals you can point
> me to, that'd be cool too.
>
> Thanks for reading all the way down to here.
>
> Jay
>
> P.S. If
A contrary view in-lined below:
On Fri, 2013-04-19 at 15:19 +0200, François Gillet wrote:
> A lot of questions, some responses below...
> > Why not explore unconstrained ordination methods and went further with
> > NMDS ("V2" mission in Anderson et al 2011)?
> >
>
> Just because your purpose is
h
> http://leba.unige.ch/team/aboissezon.html
>
> De : fgill...@gmail.com [fgill...@gmail.com] de la part de François Gillet
> [francois.gil...@univ-fcomte.fr]
> Date d'envoi : samedi 20 avril 2013 10:59
> À : Gavin Simpson
> Cc: Aurélie Boissezo
iversity of British Columbia
>
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Dr. Gavin Simpson [t] +44 (0)20 7679
in the envfit process.
As for the species scores; metaMDS adds these as a convenience feature
if the species data is available to it. They are added as a weighted
average of the site scores and then possibly expanded.
G
> thanks for any input on this!
>
> adrien
--
Gavin Simpson,
to discriminate between groups that you have defined a
priori, then a random forest is one of the machine learning tools that
might usefully be applied.
HTH
G
--
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Adjunct Professor, Department of Biology[f] +1 306 337 2
ith only three levels as a random effect there is no reason
not to use it for `strata` in the permutation test if the null
distribution you are testing needs to retain the archipelago-based
clustering of samples.
HTH
G
--
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Adjunct Pro
> City of Charlotte Storm Water Services
> Water Quality Modeler
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> Charlotte, NC 28202
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> Fax: 704.353.0473
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> last code block with the analysis of the residuals. But is this a valid
> method? I feel both structures apply in a theoretical sense; it's just a
> question of how to specify this in R.
>
> 4. Finally, an easy one, can anyone comment on the strong correlation between
> the intercept a
is
> more likely to be similar to yesterday than the day before. There is
> autocorrelation and random fluctuation, hence it makes sense to model
> it this way. For the record, as simple AR1 model better account for
> the seasonal fluctuation than a gam, and my ARMA(2,0) model does an
&
wrong and it is probably very simple to solve
> but I've got stuck on it for a while and would appreciate some help solving
> it.
>
> Thanks
> Per
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______
between plots). This runs,
> gives reasonable results that agree with the graphs, but is it
> statistically valid?
>
> Thanks,
> Jonathan
>
> From: Gavin Simpson [gavin.simp...@ucl.ac.uk]
> Sent: July 17, 2013 10:06 PM
> To: Henkelman, Jonathan
> Cc: r-s
rror 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
like to be able
> to produce something similar.
>
> Cheers,
> Jonas
>
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e same plot on my own (though with different graphic
> parameters)
> # calculate the PCoA ordination sites' scores
> pcoa<- cmdscale(dis)
> # plot them with different symbols for groups
> plot(pcoa, asp=1)
> # and add spiders and hulls
> ordispider(pcoa, groups)
> ordihull(
island.NMDS, display = 'sites')
>
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; What will the dune.env be in the case of metaMDS instead of rda?
>
> Thank you again
>
> Elaine
>
>
> On Tue, Aug 20, 2013 at 12:08 AM, Gavin Simpson wrote:
>>
>> I have some posts on my blog that explain how to do this, ain the vein
>> of Vit's reply
MDS, display = 'species', pch = '+', cex = 0.6)
>
> # sites as text
> text(NMDS, display = 'sites')
>
> Elaine
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>
0 0 0 ...
> [list output truncated]
> - attr(*, "row.names")= int [1:450] 1 2 3 4 5 6 7 8 9 10 ...
>
> I have no idea why are the species names missing, there are no warning. I
> only found questions regarding missing species scores, but that doesn't seem
> t
t;
>
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es in the CCA ordination?
>>
>> --
>> "The cure for boredom is curiosity. There is no cure for curiosity." --
>> Dorothy Parker
>>
>> ___
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e, Ph.D.
>> Research Ecologist
>> The Wilderness Society | Northern Rockies Regional Office
>> 503 W. Mendenhall, Bozeman, MT 59715
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est Regards
> Rajendra M Panda
> School of Water Resources,
> Indian Institute of Technology Kharagpur
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to do it, I would really
> appreciate it.
>
> Thanks in advance.
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> 2009-06-18,-3.97671552612412
> 2009-07-09,-3.40185954003936
> 2009-08-19,-3.44958231694091
> 2009-09-24,-3.86508161094726
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> 2010-02-11,-3.78064756876257
> 2010-03-24,-3.5823501176064
> 2010-04-27,-4.3363571587
> 2010-05-17,-3.905
nd a first pass suggests it works
> with this data. I can't quite figure out how I would go about interrogating
> the fitted spline to deterine when the peak value happens with respect to
> DoY. Any suggestions?
> -Jacob
>
>
> On Tue, Mar 25, 2014 at 9:06 PM, Gavin Simpson wro
> PhD Student
> Department of Biological Sciences
> University of Notre Dame
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; email:
> 1)visual appoach
> plot(mod$gam, pages = 1)
>
> 2) quantitative approach
> pred <- predict(mod$gam, newdata = newdat, type = "terms")
> take <- which(pred[,"s(DoY)"] == max(pred[,"s(DoY)"]))
> or
> take <- as.numeric(which.max(pred
gt;> contribute most to the dissimilarity between fish, reaches, and
>> >>basins?. I
>> >> was thinking the SIMPER procedure but am not yet sold.
>> >>
>> >> Any advice is appreciated!
>> >> --
>> >> Brandon Gerig
>> >> PhD Student
recommend a procedure to identify the congeners that
>>>>> contribute most to the dissimilarity between fish, reaches, and
>>>>> basins?. I
>>>>> was thinking the SIMPER procedure but am not yet sold.
>>>>>
>>>>> Any advice i
ment of Biology
> PO Box 1848
> University of Mississippi
> University, Mississippi 38677-1848
> Brewer web page - http://home.olemiss.edu/~jbrewer/
> FAX - 662-915-5144
> Phone - 662-915-1077
>
>
>
>
> On 3/27/14 10:47 AM, "Gavin Simpson" wrote:
>
ia SkypeI am
>
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U Octave (free, libre, opensource) to do
> it with the original MatLab code, as Octave is compatible with MatLab.
> HTH.
> Martin
>
> Gavin Simpson píše v Pá 28. 03. 2014 v 20:44 -0600:
>> In short, no. I haven't ported the rough code for LOO CV of CCA or
>> CCA-PLS mo
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>
>
>
> --
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> Research Wildlife Biologist/Statistician
> USGS Northern Prairie Wildlife Research Center
> E-mail: gsarge...@usgs.gov
> Phone: (701) 253-5528
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aries according to "species".
>
> Can somebody tell me what I am doing wrong here?
>
> I use R version 3.1.1 (2014-07-10) with vegan_2.0-10
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> Many thanks
>
> Arnaud
>
>
>
>
>
> --
> View this message
ew CRAN version
> of vegan later this month, and the R-Forge version is very close to the
> release version. (Looks like the build system is down again in R-Forge, and
> has been for a week, so that this is not the most recent and stable version
>
am Main,
> Germany
>
> Tel: +49 69 7542 1863
> Mobile: +49 1515 888 5440
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>
>
> __
On 17 October 2014 10:04, Bob O'Hara wrote:
> On 10/17/2014 05:36 PM, Gavin Simpson wrote:
>
> On 17 October 2014 06:44, Bob O'Hara wrote:
>
>> On 17/10/14 13:54, "José M. Blanco Moreno" wrote:
>>
>>> Dear users
>>>
>>
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79 0 0.000 0.0002185 ***
> > ---
> > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> >
> > cheers
> >
> > Andy
> > [[alternative HTML version deleted]]
> >
> > _______
> >
14:00, Jari Oksanen wrote:
>
> On 23/10/2014, at 18:17 PM, Gavin Simpson wrote:
>
> > On 22 October 2014 17:24, Chris Howden
> wrote:
> >
> >> A good place to start is by looking at your residuals to determine if
> >> the normality assumptions are being
ish.
I hope I've done a better of job of i) not annoying you with poorly chosen
words, and ii) explaining why I think you should stop with the current
model as is it is too complex for your data. You can;t test for an
interaction but you could remove the interaction and just test for main
effec
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> Tel. +49 6341 280 31552
>
> http://www.uni-koblenz-landau.de/campus-landau/faculty7/environmental-sciences/landscape-ecology/Staff/eduardszoecs
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> ___
> R-
Transformations. You
won't get exactly a CCA by doing RDA on chi-square transformed data, but it
will be close. You can also use the Hellinger transformation which worked
well in the tests that Legendre & Gallagher did in their paper.
>
> Thank you very much! as you can see, i am not real
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452
> ERBL2 NaN NaN
> ERNA10 -0.61157997 0.47464632
> NEST5 0.87499085 -0.04070596
> PREM -0.90401815 1.25730322
> PRVI NaN NaN
> PUTR2 0.16079095 -0.36676073
> RICE -0.35775047 -0.46386377
> ROWO NaN NaN
> SYAL2 NaN NaN
> SYO
bsu.edu
> jcbecker42 at gmail.com
>
> Call
> Send SMS
> Add to Skype
> You'll need Skype CreditFree via Skype
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However, in addition to variables in the data frame given in data=, you can
> mix variables in the work environment in your formula. If you think you
> need to have several data frames for the data= argument, please consider
> cbind().
>
> cheers, Jari Oksanen
>
&
t; University of California, Berkeley
> http://noahwhiteman.org/tim-oconnor.html
>
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(506) 8706 - 4662
>> >> Personal website: Lobito de r?o <https://sites.google.com/
>> site/lobitoderio/ <https://sites.google.com/site/lobitoderio/>>
>> >> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/ <
>> http://www.icomvis.una.ac
4662
>>> >> Personal website: Lobito de r?o <https://sites.google.com/site
>>> /lobitoderio/ <https://sites.google.com/site/lobitoderio/>>
>>> >> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/ <
>>> http://www.icomvis.una.ac.cr/>>
>>> >
>>> >
>>> >
>>> > --
>>> > Manuel Spínola, Ph.D.
>>> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>> > Universidad Nacional
>>> > Apartado 1350-3000
>>> > Heredia
>>> > COSTA RICA
>>> > mspin...@una.cr <mailto:mspin...@una.ac.cr>
>>> > mspinol...@gmail.com <mailto:mspinol...@gmail.com>
>>> > Teléfono: (506) 8706 - 4662
>>> > Personal website: Lobito de río <https://sites.google.com/site
>>> /lobitoderio/>
>>> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> R-sig-ecology mailing list
>>> R-sig-ecology@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>
>>
>>
>>
>
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspin...@una.cr
> mspinol...@gmail.com
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
--
Gavin Simpson, PhD
___
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
y mentions staggered entry. That might
be of use?
HTH
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London
nager. If by 'PC' you meant MS Windows, then John Fox and Vincent
Goulet both have useful info to help you get started, both a linked to
from the ESS web site:
http://stat.ethz.ch/ESS/
HTH
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson
h R from Tinn-R.
> >
> > ___
> > R-sig-ecology mailing list
> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
> > ___
> > R-sig-ecology mailing list
>
macs + ESS and JGR are the only cross platform options of the
ones listed.
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
G
utionary Biology Program
> > Cornell Lab of Ornithology
> > Cornell University
> > Ithaca, NY 14853-2701
> > DLR32Xcornell.edu (X = @)
> > ph 607 592 4636
> > fax 607 255 8088
> >
> > new website:
> > http://www.eeb.cornell.edu/Rabosky/dan/main.html
> >
> >
> &
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