?
Cheers, Jari Oksanen
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r-project.org]
on behalf of Duarte Viana [viana.s...@gmail.com]
Sent: 11 June 2012 21:47
To: Sarah Goslee
Cc: r-sig-ecology@r-project.org
Subject: [R
to isoMDS(), but still not
identical. For true replication of the book results you should set 'engine =
isoMDS'.
As usual, these are documented features.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi
, like your original code. You need some
changes to also return the estimated parameters.
The fitted totals are now closer to observed totals, but not identical.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r-project.org
, RDA) from community composition, also
with 'newdata' communities.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r-project.org]
on behalf of Marc Taylor [marchtay...@gmail.com]
Sent: 23 May 2012 10:19
To: r-sig
' (which can be
FALSE or SD of variables) of your original variables, and applies those to your
'newdata' before rotating to PCs.
Cheers, Jari Oksanen
From: Marc Taylor [marchtay...@gmail.com]
Sent: 23 May 2012 11:55
To: Jari Oksanen
Cc: r-sig-ecology@r-project.org
added that as an option for svd() in
cocorresp or vegan as it is documented only as a compatibility option for old
R. However, you can try editing the files to use LINPACK = TRUE to see if the
problem vanishes (but NAMESPACE add some pain in using edited files).
HTH, Jari Oksanen
in such a case, but it will change the sum of
all eigenvalues, as well as eigenvalues of axes, and scores. So it is only the
rank of the solution that is invariant with removing one species, but all other
results will change. Don't do this if you can.
Cheers, Jari Oksanen
your axis parallel to the fitted vector which you can do).
The NMDS is based on Bray-Curtis, but it is not the same, and the vector
fitting is based on NMDS. So why not write that is about NMDS? Why to insist on
Bray-Curtis which is only in the background?
Cheers, Jari Oksanen
--
Jari Oksanen
Alan,
Use vegan command
vegandocs(decision)
and look at the chapter on scaling of RDA scaling. This explains both the
scaling and how to change the scaling.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r
. Thanks!
In vegdist, the actual BC is calculated in C code. Do you mean that you have
written new C code for this special variant or are you deriving your index from
pairwise dissimilarities?
Cheers, Jari Oksanen
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was silently wrong with
non-integer data, and truncated real values to integer.
Cheers, Jari Oksanen
On 25 Apr 2012, at 17:33, Brian Inouye wrote:
Although rounding to the nearest integer will make the code run without an
error, it seems like then you are making the implicit assumption that every
. Probably
it should: the error would still be there, but the message would be more
informative.
Cheers, Jari
--
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distances a couple of years ago after I was in a workshop with Susan
Letcher, and she suggested I do this.
Cheers, Jari Oksanen
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, but such amendments could be
added to vegan if anybody contributes a patch (and in case anybody wants to do
this, the easiest source to work with may be at
http://github.com/jarioksa/vegan).
By the way, Bray-Curtis and Jaccard should have identical rank-order.
Cheers, Jari Oksanen
:
- if you want to know the rarefied richness of single plots, use rarefy().
- if you want to know which plots belong to which mhab5 data, look at your data.
Cheers, Jari Oksanen
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On 28/03/2012, at 18:59 PM, cristabel.duran wrote:
On 03/28/2012 05:36 PM, Jari Oksanen wrote:
thank you for your help. I want to know the rarefied richness of single
plots.
and I just now rarefied my data within each factor level with rarefy(), and
I got what I was looking
an idea, and even has documented this: look ?metaMDS and
vegandocs(FAQ) which both explain this in vegan.
Wouldn't that be self-evident? Stress is a proportional measure, and if a
proportion is 1, it must a percentage.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
species in the same genus as identical (dissimilarity = 0) unless you also have
a factor for species. In contrast, vegan::taxa2dist will not give zero
dissimilarities, but all rows will be regarded as different (species).
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014
. Look at the model in
vegan:::plot.taxondive to see how simple it is.
Cheers, Jari Oksanen
I argued
that I only 15 points, instead of 24 that is the overall sample number,
becasue there is an overplotting...do is it possible?
Moreover, there is the possibility to plot in the funnel diagram
-1.56716987
Do you have any idea about this error?
So what is the error?
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
solution is to request only one axis when there is only one axis:
use argument 'choices':
p1 - ordiplot(Ordi, choices=1)
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
in the development branch, and we need to clean
the table with minor stable releases to be able to have a larger update of
vegan (to 2.2-0).
Cheers, Jari Oksanen
On 29/04/2011, at 13:03 PM, Eduard Szöcs wrote:
Hai Kari,
as far as i know SimPer is not available in vegan.
I have written
this disagree with your reading?
Cheers, Jari Oksanen
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want to have
something more?
Cheers, Jari Oksanen
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something else and cannot be done light-heartedly.
Cheers, Jari Oksanen
On 23/12/2011, at 21:49 PM, Gavin Simpson wrote:
Hi Matt,
Would you mind sending me the data *off list* so I can see if I can
reproduce. The failure is within a basic part of the R stack (Lapack
matrix algebra code supplied
(communitydat, bray)'. Is this only misleading or a user error? The
file name sounds like you already had dissimilarities as the input, and if
this is the case, you should not calculate dissimilarities of
dissimilarities.
Cheers, Jari Oksanen
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On 28/11/2011 17:33, Canning-Clode, Joao canning-clo...@si.edu wrote:
Dear list,
I am kind of new to R. I want to fit the nonlinear Morgan-Mercer-Flodin (MMF)
growth model in a species accumulation curve (SAC) run with vegan package in
.R. I would very much appreciate if you could give
for me.
However, like Gav said, this may not be a meaningful test (but still
calls for a fix in vegan). If I remember correctly, Marti Anderson had
interactions in her software, but that was dropped from current
versions.
Cheers, jari oksanen
For the dune dataset, the above error occured
(). Although I said that adonis() does not do MANCOVA,
you can get the same F-values but with permutation statistics if you use
Euclidean distances:
adonis(dist(Y) ~ Year*(Lat + Lat2))
However, that should not be called as MANCOVA (because it is not
MANCOVA).
Cheers, Jari Oksanen
Con fecha 25/11
On 25/11/2011 18:26, Michel Rapinski mrapi...@uottawa.ca wrote:
Thanks for the help.
What exactly is it called if it is not a MANCOVA and how does it differ
from a true MANCOVA?
What about a (multiple) linear model?
Cheers, Jari Oksanen
or get a latest version of ordiarrows from
http://vegan.r-forge.r-project.org (I uploaded a new version with an
option to re-order points within groups some minutes ago as revision
1985).
Cheers, Jari Oksanen
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] A2 A3 A4 A5 ...
.. ..$ : chr [1:19] PCNM1 PCNM2 PCNM3 PCNM4 ...
$ values : num [1:29] 71640230 66080002 58129580 29179643
16447538 ...
$ weights : num [1:30] 1 1 1 1 1 1 1 1 1 1 ...
$ threshold: num 1092
- attr(*, class)= chr pcnm
Cheers, Jari Oksanen
?
Cheers, Jari Oksanen
First about defining an rda() model.
On 22/09/11 22:03 PM, Sibylle Stöckli sibylle.stoec...@gmx.ch wrote:
Dear R users
I am calculating a RDA for a dependent matrix (different variables for
tree performance) and different explanatory variables (species
identitiy
- metaMDS(bryceveg)
ordisurf(m ~ slope, brycesite, knots=1, bubble=4)
plot(envfit(m ~ slope, brycesite))
Cheers, Jari Oksanen
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(varechem)
mod - rda(varespec ~ Al + P + K, varechem)
## species--environment correlation
spenvcor(mod)
## interset correlation
intersetcor(mod)
## correlations among constraints (why?)
cor(model.frame(mod))
HTH,
Jari Oksanen
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you dispersion for classes: I have no idea what is the SD of
*dissimilarities* (and the same applies for the averages of
dissimilarities), but betadisper() gives you meaningful values.
Cheers, Jari Oksanen
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constant within strata, you can get high R2, but no
significant results. You know your data best (and you have access to your
data), so check yourself.
Cheers, Jari Oksanen
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in which case it is outside 95%
of the permuted values?
Cheers, Jari Oksanen
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not be
the most effective one if you want to reduce the influence of most abundant
species that usually contribute most to the total variance.
Cheers, Jari Oksanen
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).
Cheers, Jari Oksanen
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^2
[1] 0.4780616
Which are identical in three decimal places to those values that AW
reported (and they reported squared values).
# The only Eigenvalue related value I find is dune.cap$tot
What about dune.cap$manova$Eigenvalues?
Cheers, Jari Oksanen
.
Perhaps they will help you.
We can start from the easier part: what makes a good class, in your opinion?
Should they be uniform? or compact? or connected? or distinct? These
criteria are contradictory and you must make your pick.
Reading a good book may help.
Cheers, Jari Oksanen
On 9/05/11 17:55 PM, Tyler Smith tyler.sm...@eku.edu wrote:
Jari Oksanen jari.oksa...@oulu.fi writes:
Why does vegan not plot species as arrows in plot? I know how to use
scores() and arrows() to create my own arrows, but it seems odd that
this feature is not built in. Is there ever
is a measure of
*multi*collinearity. Removing some other variables than those two key ones
may reduce the VIF of the remaining. Construct your model carefully.
If the VIF still disturbs you, don't calculate the VIF.
Cheers, Jari Oksanen
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?envfit, ?ordisurf.
Cheers, Jari Oksanen
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useful data directly.
I also wrote a small funny test on TWINSPAN principle, where the splitting
and pre-defined pseudospecies where replaced with regression tree split.
I'll send you a copy of that and the FORTRAN (IV, I think) code I have in a
separate message.
Cheers, Jari Oksanen
of
the project after the initial contact.
I do think that Twinspan is a suboptimal choice for classification problems,
but I won't go into details. I urge you to study its behaviour yourself if
get your hands on Twinspan.
Cheers, Jari Oksanen
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haven't done that yet (contributions are welcome
and will be credited in the documentation).
Cheers, Jari Oksanen
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out how to perform a BVSTEP,
So what is BVSTEP?
Cheers, Jari Oksanen
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'
as you can see if you read the help page ?metaMDS (which may not be a bad
idea).
Cheers, Jari Oksanen
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not occur in your data) will influence your data. That is
only informational, and not an error.
Cheers, Jari Oksanen
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, and these become inadequate for
variables used in stratified sampling.
So the answer to question one: don't use the same variable in the model that
you have as a stratum.
Cheers, Jari Oksanen
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factors.
Cheers, Jari Oksanen
Thanks in advance for clearing this up.
Cheers,
A
--
View this message in context:
http://r-sig-ecology.471788.n2.nabble.com/adonis-with-continuous-variables-tp6
155914p6157029.html
Sent from the r-sig-ecology mailing list archive at Nabble.com
, you can
proceed like this:
xy - with(varechem, cbind(pH, Humdepth))
xy - scale(xy)
# check: cor(xy)
# consider: xy - scores(prcomp(~ pH + Humdepth, data=varechem, scale=TRUE))
ord3 - metaMDS(varespec, k=3)
pro - procrustes(xy, ord3) # will re-scale scores of ord3!
rot3 - fitted(pro)
Cheers, Jari
permutation. I have no idea of your hypothesis, though, and I can't help
here.
Cheers, Jari Oksanen
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occur on
your site or then not (begins to sound as a tricky as trying to say is you
is or is you ain't my species).
Cheers, Jari Oksanen
On 5/03/11 00:40 AM, Michele Tobias tobias.mich...@gmail.com wrote:
Hello,
I'm building species response curves for several species (one curve for
each species
of the
capabilities() command: are items tiff and cairo TRUE or FALSE?
Cheers, Jari Oksanen
On Tue, Feb 22, 2011 at 12:16 PM, Howe, Eric (MNR) eric.h...@ontario.ca
wrote:
Good day list members,
I can't save my plot as a .tiff using Cairo (error message: not
supported) or the tiff() function
On 21/01/11 15:32 PM, Martin Unterseher
martin.unterse...@uni-greifswald.de wrote:
Dear Jari,
thank you for your help. The plots are fine and really valuable.
However, when I tried to generate a Sweave-based file, all plot()
commands following poolaccum() (e.g.
\begin{figure}
fig=true
, and since you use lattice graphics, you
must print() it. This works:
\begin{figure}
fig=true,echo=false=
pool.test-poolaccum(test)
print(plot(pool.test))
@
Cheers, jari oksanen
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be considered for pairwise
comparisons. A separate set of tools is needed for pairwise comparison
in this context, and we do not provide those tools (but contributions
are welcome).
Cheers, Jari Oksanen
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Martin,
I have supposed that functions poolaccum() and estaccumR() do this. If
they are not suitable for your needs, please tell me what you want to
achieve.
These two functions have been in vegan since release 1.15-4 (7
September, 2009).
Cheers, Jari Oksanen
On Tue, 2011-01-18 at 09:22
(different farms) of the
transects, and that seems to work well.
Thanks much
Your tutorial is very helpful as well.
Michael Wilson.
University of Tennessee
From: Jari Oksanen [jari.oksa...@oulu.fi]
Sent: Friday, December 17, 2010 12:37 AM
). Therefore I'd
like to think a bit before I release these functions: there is a danger
people may use them...
Cheers, Jari Oksanen
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use functions like lm(), glm(), nls(),
gam() or some hundred other alternatives in packages to analyse the results.
Cheers, Jari Oksanen
-Burak
From: Andy Rominger [mailto:ajromin...@gmail.com]
Sent: Tuesday, November 23, 2010 4:11 PM
To: steve_fried...@nps.gov
Cc: Pekin, Burak K; r-sig
PERMANOVA standalone software binaries in Windows), you can use
adonis() of vegan which does this like it should be done.
Cheers, Jari Oksanen
-Original Message-
From: Jari Oksanen [mailto:jari.oksa...@oulu.fi]
Sent: Wednesday, November 24, 2010 5:35 PM
To: Pekin, Burak K; 'Andy
was your problem, so we have no idea if you had a
meaningful analysis.
Cheers, Jari Oksanen
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to the
surface:. The full space analyses by Marti Anderson even handle the
imaginary dimensions (associated with negative eigenvalues in metric MDS)
within the function which may be very hard to handle with explicit PCoA.
Cheers, Jari Oksanen
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dissimilarities you will have some negative eigenvalues. These
are ignored in db-RDA (capscale), but they are taken into account in adonis.
Which method to use depends on your questions, and what else you want to do
with your data than get the test statistics.
Cheers, Jari Oksanen
of pcnm() functions (it seems that
one line is enough).
I think CCA and adonis is not a good coupling: CCA is weighted method using
Chi-square metric and adonis is unweighted using Euclidean metric. Coupling
RDA and adonis or capscale() and adonis (for non-Euclidean case) is more
natural.
Cheers, Jari
zero columns (any(colSums(tmp) = 0)).
Cheers, Jari Oksanen
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packages) using
install.packages(gravy, repos=http://r-forge.r-project.org;)
or selecting the repository address in the GUI installer.
The package is unreleased and experimental, and there may be rough edges.
Proceed with care.
Cheers, Jari Oksanen
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of the above-zero count
data, use the truncated negative binomial model offerred by
pscl::hurdle(). It is designed for the purpose (and has a more exciting
narrative for ecologists).
Cheers, Jari Oksanen
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On Wed, 2010-08-18 at 11:14 +0300, Jari Oksanen wrote:
On Wed, 2010-08-18 at 09:50 +0200, Opdekamp Wout wrote:
Hi all,
In Primer/permanova+ it is possible to get the pearson correlation of a
species with the axes of NMDS or capscale. Is it possible to extract or
calculate these as well
the warning. That's life, but no reason to worry.
You can see this by looking and plotting the results.
Cheers, Jari Oksanen
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don't know yet
if this is just like it should be or should we do something with this.
Cheers, Jari Oksanen
On 10/08/2010 1:21, Adriano Melo grumi...@yahoo.com.br wrote:
Dear colleagues,
I and a graduate student (Fabiana Schneck) are using the adonis() function in
vegan to test for the effect
:
update(m, . ~ . - Use)
As usual, contributions are welcome.
Cheers, Jari Oksanen
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in selecting the species to
display?
I will be very grateful for any help.
HTH, Jari Oksanen
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or negative data while you are fairly
sure that you don't have them, the common rule is that you're wrong and R
is right. Check your data to see that it is like you expect it to be. This
is not an issue to argue with computers: they always win.
Cheers, Jari Oksanen
seems not to work.
1 - cor(dat) ## dissimilarity
Actually the canonical transformation to distance is sqrt(2-2*cor(dat)).
Cheers, Jari Oksanen
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?
Cheers, jari oksanen
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() that is used instead of the one in vegan. Which
one of the competing versions of scores() is used depends on the order
they are loaded and attached, and how the different scores() are located
in the search path. -- If scores() is the problem.
Cheers, Jari Oksanen
of this is completely untested.
Cheers, Jari Oksanen
PS. When you ask for the advice on non-standard commands defined only in
packages, you should tell us what are the packages involved. In this case,
metaMDS and ordisymbol are in different packages so that you need extra care
in their interface, and you should
arrows and labels, and points() only
unlabelled arrows.
See ?text.cca, ?points.cca for details and further arguments.
Cheers, Jari Oksanen
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On 26/04/10 13:42 PM, Christine Griffiths
christine.griffi...@bristol.ac.uk wrote:
Dear All,
I have done pairwise comparisons of species compositions between three
treatments (1 v 2, 1 v 3, and 2 v 3) which were replicated 6 times (i.e. 6
blocks). To avoid multiple testing I have decided to
, but there is an improved way. Check ordistep()
for Canoco-style analysis, and add1.cca, drop1.cca for another ways.
Cheers, Jari Oksanen
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the error message you got from
scale.default.
HTH, Jari Oksanen
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-emptiness. You have other tools for this, like looking at the object (or
writing a query to a mailing list).
Cheers, Jari Oksanen
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, Jari Oksanen
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.
Cheers, Jari Oksanen
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and env: only two observations were left in the example subset
you had in your message. I'm not sure that so fragmented models are
meaningful.
Best wishes, Jari Oksanen
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On 19/01/10 10:17 AM, Roman Luštrik roman.lust...@gmail.com wrote:
Thank you Jari and Ben.
I have tried something along the lines what Ben suggested but stopped and
asked here if there's a better way, as I didn't want to invent the wheel
(yet crude one).
Roman,
I think the only sustainable
sets have 2.5 dimensions (Kruskal).
Cheers, Jari Oksanen
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and add an
argument for the purpose.
Cheers, Jari Oksanen
Here is the code I use if of any help:
cca.plot3d - ordiplot3d(CCA, type=h, angle=40)
text(cca.plot3d, points, pos=c(4, 4, 2, 4, 3, 4, 2, 2, 4, 2))
text(cca.plot3d, arrows, cex=0.7)
points(cca.plot3d, points)
Cheers,
Roman
(not totals) fixed (thus fill, too);
3) abuswap: row and column occurrences (and so the fill) fixed, and
row OR column totals (this latter algorithm was published by Hardy
2008 J Ecol 96, 914-926).
Maybe this abuswap is the closest to the one you wanted.
Cheers, Jari Oksanen
. Would I be a
referee or an editor for this kind of ms, I would be very skeptical ask for
the proof of the validity of the null model.
Cheers, Jari Oksanen
I don't see this as being a
real
problem with the large matrices I'll deal with though, but
definitely
something to be aware of.
If you're
appreciated...thanks
Jason,
Is it sufficient to draw lines with graphical par()ameter xpd = TRUE? For
instance,
plot(0:1, 0:1, type=n)
segments(-1, -2, 2, 2, col=2, xpd=TRUE)
lines(c(-0.1, 1.1, 1.1, -0.1, -0.1), c(-0.1, -0.1, 1.1, 1.1, -0.1), xpd=T)
abline(0, 1, xpd=TRUE)
Cheers, Jari Oksanen
that in no case would the 'station' change in fitted models
and all permutations would have identical statistics (within numerical
accuracy).
adonis() does not have plot method, but you can use betadisper for plots.
Cheers, Jari Oksanen
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