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That is not that useful as you need to give the software something
about when the samples occur in time, otherwise it doesn't have the
information needed to properly model the decay in correlation with
time.
You need to give it the observation time, however you measured it.
HTH
G
?
>
> Does anyone have experience with this, and can explain how I should do
> it properly?
>
> Mark
>
> __
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he 'distance' argument
>
> Best wishes
> Tom
>
>
>
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m the R help mailing list archive at Nabble.com.
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide co
up on this)
for a (far) more authoritative answer on this part of your question.
HTH
G
>
> Thank you very much for answering!
>
> Best wishes,
> Christoph
>
>
--
Gavin Simpson, PhD [t] +1 306 337 8863
Adjunct Professor, Department of Biol
> X.dist1 <- metaMDSdist(X, method="bray",zerodist = "ignore")
> X.dist2 <- metaMDSdist(X, method="bray",zerodist = "add")
>
> Can Please help me with this.
> Thanks,
> Mitra
>
> [[alternative HTML version deleted]]
>
> __
> not support a direct model comparison to test the significance of the
> random effects. I'm guessing the best strategy based on the summary.gam
> is probably just to compare fit indices like Log Likelihoods.
>
> If anyone has any other suggestions, though, please do let me know.
t; Formula: ~1 | g/xc
> Parameter estimate(s):
> Phi
> 0.1809409
> Variance function:
> Structure: fixed weights
> Formula: ~invwt
> Number of Observations: 264
> Number of Groups:
> g xc %in% g
> 134
>
> $gam
>
> F
logy/attachments/20130419/114d1e5f/attachment.pl
HTH
G
--
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.simp...@uregina.ca
523 Research and Innovation Centre
** performed an NMDS. Not sure why
Jari labelled these as "MDSx". If this bothers you so, add your own
labels:
require("vegan")
data(dune)
sol <- metaMDS(dune)
plot(sol, xlab = "NMDS1", ylab = "NMDS2")
HTH
G
--
Gavin Simpson, PhD
ations" are random
starts, each of which has iterations of the algorithm.
HTH
G
> parth.mds <- metaMDS(WorldPRSenv, distance = "bray", k = 2, trymax = 100,
> engine = c("monoMDS", "isoMDS"),
> autotransform =TRUE, wascores = TRUE, expand = TRUE, tra
c à Rimouski
> > remilesmeri...@yahoo.ca
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do
..@yahoo.ca
>
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> and pro
arametric factor terms what the intercept is depends on
the contrasts used - the default in R would represent the mean of the
response for the reference level(s) of factor terms in the model.
The intercept is separates from the penalised spline terms in the model.
HTH
G
--
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> and provide commented, minimal, self-contained, reproducible code.
--
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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
t; >
> > >
> species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species,
> dis="sites")plot(ef,p.max=0.1)
> > > > > Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical
> > > subscript too long
> > > > > Many thanks!
> > > > > Laura
> > &g
nger than the object
being subscripted.
I promise to delete the data once I have tracked the problem down.
Cheers,
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geograph
rs[,2] * mul, length = 0.05,
col = "blue")
text(scrs * mul * 1.1, labels = rownames(scrs), cex = 0.9,
col = "blue")
Not that I recommend this "pruning" a CCA...
HTH
G
--
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Dr. Gavin Si
abble.com.
>
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> and provide commented, minimal, self-contained, reproducible code.
>
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Dr. G
version deleted]]
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> and provide commented, minimal, s
tions!
>
>
> Matt
>
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> and provide commented, minimal, se
g the following warning message
> after model completion for larger models (with many more variables
> than 2):
>
> Warning message:
> In mer_finalize(ans) : false convergence (8)
>
>
>
>
> Thank you for your time, effort, and patience dealing with a novice.
>
> Sin
ve at Nabble.com.
>
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> and provide commented, minimal, self-containe
suitable editor which can break the
> command properly.
>
> All the best
>
> On 13 April 2012 19:33, Gavin Simpson wrote:
> > On Fri, 2012-04-13 at 17:46 +0800, Wincent wrote:
> >> Dear useRs,
> >>
> >> I am writing a vignette for a package,
ke lines
where it could.
In short get out of the habit of writing long lines of R code; you'll be
better in the long run laying your code out logically.
HTH
G
--
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Dr. Gavin Simpson [t] +
ted, minimal, self-contained, reproducible code.
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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
Go
ect.org mailing list
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r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC
tested as there wasn't reproducible code, but hopefully
you'll be able to work it out from the above.
HTH
G
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679
contained, reproducible code.
> >
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/I-cannot-get-species-scores-to-plot-with-site-scores-in-MDS-when-I-use-a-distance-matrix-as-input-Pr-tp4103699p4104406.html
> Sent from the R help mailing list archive at Na
ww.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] g
hoose(150, 10)
[1] 1.169554e+15
??
G
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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 Stre
he
code yourself using functions from permute).
HTH
G
> thanks,
> René
>
>
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.
in advance,
> René
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, re
cable any that don't apply. ;-)
> Peter Ehlers
>
> On 2011-11-16 12:12, Gavin Simpson wrote:
> > On Wed, 2011-11-16 at 14:29 -0500, R. Michael Weylandt wrote:
> >> Suppose your matrix is called X.
> >>
> >> ? sample
> >> X[sample(nrow(X))
SE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> __
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As a general matter of routine practice, I don't think this is a very
good way of working, especially as we have no good ecological grounds
for doing so and who knows what information these species could be
telling us if we just listened to them instead of discarding them.
HTH
G
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Dr. G
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t;HAL7","DOH1","DOH2","DOH3","DOH4","DOH5")
> > fish.pca <-rda(fish.sqrt.h)
> > fish.site <- scores(fish.pca,display="sites",scaling=3)
> > fish.spp <-
> scores(fish.pca,display="species",scali
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in this.
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/binomial-GLM-quasi-separation-tp3901687p3904261.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailin
about-GAMs-tp3900848p3901842.html
> Sent from the R help mailing list archive at Nabble.com.
>
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chive at Nabble.com.
>
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hz.ch/mailman/listinfo/r-help
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Dr. Gavin Simpson [t] +44 (0)20
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%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
ne who can help me as I have asked people who
> use R near me and no-one is sure and uses Adonis..
>
> Ash
> __
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> PLEASE do read the posting guide h
symbols of
> >>>> the points and the line.
> >>>>
> >>>>
> >>> If it's OK to have the lines going right though the symbols, then
> >>> go ahead,
> >>> hack the code. All you need to do is add ,"o" to the type
> >>> argum
ing guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpso
ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Dr. Gavin Simpson [t] +44 (0
; I am using R 2.13.1 on a PC inside RStudio.
>
> I realize I can do this in package mgcv, but just curious as to
> whether this is something known and fixable?
>
> Thanks
>
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson
oices = c(1, 2)..." which seems to suggest the function might not
> allow a third axis at the moment?
> Cheers,
> Briony
>
>
> On Tue, Sep 13, 2011 at 2:53 AM, Gavin Simpson [via R] <
> ml-node+s789695n3807984...@n4.nabble.com> wrote:
>
> > On Mon, 2011-09-12
_
> > >>> r-h...@r-project.org mailing list
> > >>>https://stat.ethz.ch/mailman/listinfo/r-help
> > >>> PLEASE do read the posting
> > >>> guidehttp://www.R-project.org/posting-guide.html
> > >>
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>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-co
g guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/envfit-vector-labels-with-ordiplot3d-tp3800669p3807015.html
> Sent from the
ever.
G
> /iaw
>
>
> Ivo Welch (ivo.we...@gmail.com)
>
>
>
>
>
> On Wed, Aug 17, 2011 at 5:18 AM, Gavin Simpson
> wrote:
> > On Tue, 2011-08-16 at 17:46 -0700, ivo welch wrote:
> >> I think I found a bug in the Cairo library, plus weird beha
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Dr. Gavin Simpson
could find it and if I need a special R
> version to do it.
packfor is part of the *sedar* project on R-forge. You can get a binary
or sources from:
http://r-forge.r-project.org/R/?group_id=195
HTH
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Si
m = ylim, xlim = xlim,
ylab = "PC2", xlab = "PC1", cex = 0.7, asp = 1,
type = "n") ## no plotting this time first
abline(h = 0, lty = "dotted")
abline(v = 0, lty = "dotted")
text(si.scrs[,1], si.scrs[,2], labels = rownames(si.scrs),
cex = 0.7) ## add site and species scores as labels
text(sp
make sure you turn on the email lists and off the
functions/vignettes.
> Thank you.
G
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building,
t does predict() not do that you are expecting?
Indeed.
G
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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, Londo
y(1:100,dim=c(2,5,10))
>
> Q <- matrix(1:10,nrow=2,ncol =5)
For this one, consider the often overlooked function `sweep()`:
sweep(Z, c(1,2), Q, "-")
does what you wanted. c(1,2) is the `MARGIN` argument over the
dimensions that Q will be swept from.
HTH
G
--
%~%~%~%~%~%~%~%~%
t;)
> > unname(z)
> [1] 2
> > z
> a
> 2
> > zz <- unname(z)
> > zz
> [1] 2
> > names(z) <- NULL
> > z
> [1] 2
>
> Cheers,
> Bert
>
>
> On Tue, Jul 26, 2011 at 1:18 PM, Gavin Simpson
> wrote:
> > On Tue
ry names(result)=NULL to get rid of the name.
>
> Barry
`unname()` exists for this purpose:
> foo <- 1
> names(foo) <- "bar"
> foo
bar
1
> unname(foo)
[1] 1
G
--
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Dr. Gavin Simpson
t.org mailing list
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> and provide commented, minimal, self-contained, reproducible code.
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC,
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Pass the returned object to dist() to get the distances you want.
HTH
G
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.
f Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> > >> University of Oxford, Tel: +44 1865 272861 (self)
> > >> 1 South Parks Road, +44 1865 272866 (PA)
> > >> Oxford OX1 3TG, UKFax: +44 1865 272595
> > >
> > >
> > &g
> .tar.gz files from those links should have full R, C and Fortran source code.
>
> I think we need counter-examples...
>
> Barry
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rm=c(0,0,0,0) , build=buildNAIRU,
> hessian=TRUE, control=list(maxit=500)))
> (dlmNAIRU <- buildNAIRU(fitNAIRU$par))
>
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>
> This is even worse. It seems like the algorithm is quite sensitive to
> starting values. Is this behavior expected or is there some flaw in the
> algorithm?
>
> Ravi.
>
>
> From: r-help-boun...@r-project.org [r-he
w.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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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
dimensions are these vectors
> > being correlated? Is there code to produce the x, y, and z coordinates of
> > each of the sites in Fish.mds?
> >
> > Thanks very much.
> > Katie
> >
> >
> >[[alternative HTML version deleted]]
> >
> >
.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> __ R-help@r-project.org mailing
> list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting
> guide
> >
> > Estimated degrees of freedom:
> > 3.9393 total = 4.939297
> >
> > GCV score: 0.002666985
> >
> > > Just out of pure academic interest. :-)
> >
> > Hope your academic curiosity is now satisfied. :)
> >
> > HTH.
> >
&g
h("EOF")
It is at times like this that an R equivalent of:
http://lmgtfy.com/
would be handy ;-)
Or it slightly cruder cousin...
G
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography
> 2011-03-30 10:42 keltezéssel, Kehl Dániel írta:
> > It helped a lot indeed, thank you very much!
> > Now I understand why it was a problem for persp!
> >
> > Daniel
> >
> > 2011-03-30 10:31 keltezéssel, Gavin Simpson írta:
> >> On Wed, 2011-03-30 at 09:55
org mailing list
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> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > David Winsemius, MD
> > Heri
0,"a1gpar"] <- NA
>
> dat0[dat0$a1pias==-999.,"a1pias"] <- NA
>
> dat0[dat0$a1devt==-999.,"a1devt"] <- NA
>
> [[alternative HTML version deleted]]
>
> ______
> R-he
>
>
>
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A "please" wouldn't go amiss there! You can remove yourself; the first link in
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je tudomásul veszi és
> hozzájárul, hogy az üzenetekhez más banki alkalmazott is hozzáférhet az EBH
> folytonos munkamenetének biztosítása érdekében.
>
>
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e=sqlFetch(STEST, "Sheet8")
> > odbcClose(STEST)
> > Spe
>
> (The species data contains the abundance of 32 species over 90 sites, set
> out like this)
>F1AmpFlavAmpWri ArcCat ArcDis
> 1 N1_1 22.2929936 0.000 0.000
reproduce SAS exactly. And I'm a little frustrated I
> can't remember the matrix command to get that multiplication done
> without cbinding the 2 columns together that way.
You might have been thinking of sweep():
sweep(scalermca[,1:2], 2, c(0.827094,-0.7644828), "*&qu
_
> R-help@r-project.org mailing list
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> and provide commented, minimal, self-contained, reproducible code.
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl
gt; > and provide commented, minimal, self-contained, reproducible code.
> >
>
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Instead of resorting to these ad-hoc approaches to correct for
overdispersion, you would be better off fitting models that model the
overdispersion. Try a negative binomial (glm.nb() in MASS) or the
zeroinfl() and hurdle() functions in the pscl package. Those all have
proper log likelihoods and you c
I was referring to is :
>
> "In case of a matrix or data frame, each row corresponds to an observation,
> and each column corresponds to a variable. All variables must be numeric.
> Missing values (NAs) are allowed."
>
> So, I'm under the impression it handles
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> _
etc), so you compute them on the link scale and apply the inverse of the
link function to get them on to the response scale.
HTH
G
>
>
>
> On Wed, Jan 26, 2011 at 11:41 PM, Gavin Simpson
> wrote:
> On Wed, 2011-01-26 at 19:25 -1000, Ahnate Lim wrote:
>
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