-values are not
missing values, but they indicate 0-difference (= identical observations). The
missing values must be coded as NA.
cheers, Jari Oksanen
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman
The varpart function does not have na.action argument, and all undefined
arguments are regarded as explanatory data sets X (they come after …).
Best wishes, Jari Oksnaen
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
ractar symbols. You can also
transform your data to to one-digit width yourself, and vegemite() will be
happy.
cheers, Jari Oksanen
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do
r unit is missing, then there are two
pieces of advice:
1. You should not do so.
2. If you want to do so, you can generate your resampling matrices
by hand and use that matrix as the argument of permutations=. See
the documentations (?adonis) which tells how to do so.
Cheers, Jari Oksanen
_
we can do in the plot line.
Have a nice week, best regards
I haven't followed this list, and therefore my answer is a bit
(a big big) late: the help page of plot function suggests to
use type=t (that is type is text) in your plot command.
Best wishes, Jari Oksanen
this by issuing vegandocs(NEWS) command after loading library(vegan).
(3) I have no idea what your script does (id does something different than
vegan::rda()) and I cannot reproduce the problem without that knowledge.
Kind regards, Jari Oksanen
PS. Sorry for not top-posting: Gmane does not allow it.
PS2
as
is your mystique implementation of pairwise distances. Your
example (ks.test()) probably would be pretty slow. If you can
vectorize your distance, it can be really fast, even if you
calculate the full symmetric matrix and throw away the diagonal and
upper triangle.
Cheers, Jari Oksanen
:::designdist we do that
for some function types, but you really must *think* about the function you are
using to know if you can write it in vectorized form. It is not automatic.
Cheers, Jari Oksanen
On 16/05/2014, at 18:46 PM, Witold E Wolski wrote:
Dear Jari,
Thanks for your reply
are well separated
from others, and probably have some disjunction with microbial taxa
that do not occur in the rest.
I suggest you do not use nonmetric MDS with nine (9) points. It may
be that metric scaling (cmdscale in R or wcmdscale in vegan) works
better.
Cheers, Jari Oksanen
scaled values (percentages), choices like 'distance = manhattan'
or 'distance = euclidean' or 'distance = gower' could work better.
As we have no reproducible example, this is all guessing.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https
to
either of these groups. However, with 8 points you should not push your
analysis too far away to firm conclusions.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http
what you mean with correcting for negative eigenvalues.
You can have transformation that removes them, but I cannot see
how that would be a correction.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
of
the method is to compare dispersions within groups. There are other
tools to compare the locations of group centroids (adonis in vegan), but
they won't give you distances.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch
observations. It worked. The results looked
sensible (i.e., they were not meaningless numerical noise). It was not fast,
though, but it can be done.
Cheers, Jari Oksanen
PS. Sorry for excessive pruning, but gmane does not allow me post if I don't
remove some quoted lines
where
this is justified (Peres-Neto et al. 2006, Legendre Legendre 2012).
Sorry for excessive pruning of your original post: I use gmane to
post and it does not allow appropriate quoting of the original
message.
Cheers, Jari Oksanen
__
R-help@r
' are distances (dissimilarities), you do not need as.dist()
for them, and the formula takes a 'data' argument, so that you can write:
capscale(dist ~ Var1 + Condition(Var2), mydataset)
I would start at looking how 'dist' and 'mydataset' look like, and what are
'Var1' and 'Var2'.
Cheers, Jari Oksanen
)
This is guaranteed to fail. Use instead
d - betadiver(dataR, sim)
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide
show?
You can add X-axis with command axis(1), but it hardly shows anything useful.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE
it is something funny in your
data.
Cheers, Jari Oksanen
on possible problems. It is up to you see if there are problems or not.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R
(PRIMER) is conducted. The user
guide does not make it clear.
I think it is best to look at the source code to see how things are really
done. This is easy in vegan which is open-source. I don't know about PRIMER.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
using an ancient version?
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting
Ecology book discusses some reason. The issue was also
discussed by Rune Økland (2003) J. Veg. Sci. 9, 693-700. I don't quite
agree with these analyses, but the margin of this page is too narrow
to contain the full analysis.
Cheers, Jari Oksanen
__
R-help@r
regularly. Legendre Legendre (2012) Numerical Ecology give
some reasons for their occurrence.
In you Venn diagram you have obviously selected an option of not
displaying negative terms. Get the full sums of the components,
including negative ones, and I bet the sums will match.
Cheers, Jari
to have NA-handling
in wascores, you better submit new code to vegan and we will incorporate
that in the next release.
Best wishes, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting
their functions to work with alien objects. Not in this case. It
neither makes sense for ade4::randtest be able to handle vegan object
because randtest does not know what to do with contional (partial)
models.
Cheers, Jari Oksanen
__
R-help@r-project.org
can plot the
profile close to the solution:
plot(profile(fisherfit(a)))
The profile() function may be able to find cases where the solution was really
bad and a better solution could be found nearby. In this case the situation
looks good.
Best wishes, Jari Oksanen
class. This may succeed with command as.dist().
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented
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
, data = dune.env, add = TRUE, knots = 1)
HTH, Jari Oksanen
PS. The density of vegan users is higher in r-sig-ecology than here:
consider posting there for a more secured answer.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r
probably get better response in r-sig-ecology.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal
(myAnova). If you want to get
printed output like in your example above, you can use
printCoefmat(as.data.frame(myAnova), na.print=, signif.legend=FALSE)
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi
. In either case, report the results to me (outside the list)
so that I know whether I managed to fix the problem or I have to find new
blind ideas.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE
for other variables, and therefore you cannot analyse
them.
Cheers, Jari Oksanen
I can see how to fix this in vegan. All I can do is to handle these cases
smoothly and with comprehensible error messages, though. They cannot be handled
with permutation tests since there is nothing to do if Constrained
probably need to go to
Canoco if you *really* need DCCA.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented
data.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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.
your error
message above). This is a function that changes 3D coordinates onto your
plotting plane. You may proceed like this:
sp - scores(ENVIESRDA, choices=1:3, display=species)
text(pl$xyz.convert(sp), rownames(sp))
HTH,
Jari Oksanen
__
R-help@r
be analysed. You
can remove these variables without influencing your fitted model, because
they really are redundant variables.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting
in metaMDS: having no.share 0 and distance = euclid
sounds dubious, and I have tried to catch those cases and issue an informative
warning. You could also try higher trymax to get more consistent NMDS results.
Cheers, Jari Oksanen
__
R-help@r-project.org
. It warned you about this.
If you want to have even those in your graph, you should use
your data as input (either step3 or step4 -- I have no idea which
one actually makes sense).
HTH, Jari Oksanen
#NMDS
step1-read.delim2(day20.txt, row.names=1)
library(clusterSim)
step2-data.Normalization(step1
(and will be credited with the function help).
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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
the original observations (rows, columns). Without knowing what kind of
results you got, I'd go for 'ncf' way of permutations (like I did in vegan).
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do
people think they are using
one package but use another when doing the top level analysis.
If there is a resolution to this, I'll be happy.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do
.
Cheers, jari Oksanen
The reason for this is that the dimension of the plot is automatically
scaled to fit the points. This distorts the visual impression of the
distances, angular relationships, and relative locations. If you plot on a
square pane, however, peace and order are restored
. Switch to regression.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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
. The following example displays some most
abundant species in the dune data set:
ord - decorana(dune)
plot(ord, type=n)
text(ord, display=species, select = colSums(dune) 20)
Ciao, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman
to
anyone before starting. Of course, if this already is in R, I won't do this.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting
) unstable, or (c) both. This means that you
should not depend on the package.
If you think that neither of these is true, but the package is both ready for
the release and stable, you should urge its developer to release (a stable
version of) the package in CRAN.
Cheers, Jari Oksanen
. Howeveer, you can flip an axis by setting its limits in xlim or ylim.
First axis is flipped by:
m - cca(dune)
plot(m, xlim = c(2, -3))
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read
without replacement.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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
both environmental and species
scores as arrows/vectors?
See ?biplot.rda in vegan.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting
On 11/10/10 15:42 PM, Nevil Amos nevil.a...@gmail.com wrote:
I am using cascaple() in vegan, is it permissible to have more than
one conditioning variable thus
capscale(DIST~varaible1+variable2+Conditon(varaible3+variable4),
data=mydata)
Nevil,
Yes, it is permissible.
Cheers, Jari
must be rectangular
(rows and columns).
Cheers, jari oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal
-sided.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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.
, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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.
to see at my leisure how to implement their methodology in
vegan. I guess it's above...
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org
the Forge woke up, and soon
after the second message it went down. Since I'm not Bayeasian, I don't know
what to say about the effect of my messages.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do
prb eco.prb at gmail.com writes:
Dear all,
I realised a correspondence analysis with function cca() of vegan library.
Just like in Okansen (2010) in the example of R help:
library(vegan)
data(varespec)
data(varechem)
vare.cca-cca(varespec~ Al + P + K, varechem)
With plot.cca()
none of these problems.
Intriguing discussions may loom round the corner...
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
this inheritance in its class(), and therefore you can
either explicitly use princomp methods or set the class to inherit from
princomp. Since biplot.princomp is not exported, you must use
stats:::biplot.princomp notation to access the biplot() function if you do not
set the class.
Cheers, Jari
$feeding), col =
as.numeric(FD.mat$feeding))
This works only with vegan functions, but you seemed to be using them.
Best wishes, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
edit pvclust() to make it
work with your choice of dissimilarity methods and other dissimilarity
functions.
Best wishes, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http
() uses divisor 'N-1' (which is implied
in ?prcomp --
this really could be more explicit).
So you see: you did not need a guru to answer you -- reading the code and docs
was sufficient.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https
phoebe kong sityeekong at gmail.com writes:
Can someone tell me how to find the center of cluster points in PCA (PC1 vs
PC2)? Can R find that out? If yes, how it's generated by R? Is the
coordinate of center point equals (mean score of PC1, mean score of PC2)?
Phoebe: Yes.
Cheers, Jari
, but the latter is
computationally more complicated and may need a special implementation for rank
deficit data. There are further complications, but I won't guess anything about
them before I get more details.
Cheers, Jari Oksanen
__
R-help@r-project.org
afford expensive thrills).
I am writing a document and would like to include a
abbreviation list (similar to ANOSIM = Analysis of Similarities).
Just go on. However, the name of the function is not necessarily the acronym of
the method.
Cheers, Jari Oksanen
suggestions are greatly appreciated!
Thank you,
Kim
Kim,
A small addition to Gavin's reply: the option of having your own dissimilarities
was added in the latest release version (1.15-4). If you do not have that in
your version of vegan, you should upgrade.
Cheers, Jari Oksanen
plans to change this). So you must
remove missing data rows manually.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
to those alternatives that Gav listed, these also mention functions
ordipointlabel (which can be further processed with orditkplot) and ordilabel.
You can also see plot.cca help which has some examples.
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
there is no exposure. The value is
missing and I can't call it 0 as 0 stands for east and west.
The cca does not run with missing values. What can I do to make vegan
cca ignoring these missing values?
Thanks a lot,
Kim
This is timely as Jari Oksanen (lead developer on vegan) has been
swertie v_coudrain at voila.fr writes:
Hello, I performed a Mantel test and plotted communitiy similarities. I
would like to add a least square line. I thought about using abline taking
as slope the r-statistic of the Mantel test and calculating the y-intercept
analytically. Is this method
the code of the function (or in a happy case, its documentation)
to see what is the scaling factor.
I checked with drawing an ellipse directly with the cov.trob data
and both of the circles fit nicely.
Cheers, Jari Oksanen
__
R-help@r-project.org
of this
ellipse.
If you have the ellipse from cov.trob(), then you could do like this
sqrt(eigen(cov.trob(mydataforellipse)$cov)$values)
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read
.
Best wishes, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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.
and different sum of all eigenvalues like
you would expect for different data sets.
I even failed to create the raw data matrix of dimensins 68000 x 6000 (Error:
cannot allocate vector of size 3.0 Gb).
Cheers, Jari Oksanen
__
R-help@r-project.org mailing list
https
don't have. In statistics, I mean. If they are invisible,
could they be made more visible?
Cheers, Jari Oksanen
De : nikolay12 nikolay12 at gmail.com
À : r-help at r-project.org
Envoyé le : Lundi, 20 Avril 2009, 4h37mn 41s
Objet : [R] PCA and automatic
(sstar / tstar);
The last line has the multiplication, the previous collect the terms for the
stress.
Best wishes, Jari Oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http
that happened to be
on my desk (Psychometrika 29, 1-27 and Psychometrika 29, 115-129, both from
1964). Both of these expressed stress in percents. Certainly this is not a
convention introduced by the authors of the package, since they are much too
young to have done that prior to 1964.
Cheers, Jari Oksanen
Jaccard is that there is a huge
number of packages that have this index, and you probably forget some of those
in any recommendation. I think at least the following packages have Jaccard
index: ade4, analogue, ecodist, labdsv and probably many more.
Cheers, Jari Oksanen
)
m0 - update(m0, . ~ . + Topo)
add1(m0, scope = formula(mbig), test=perm)
m0 - update(m0, . ~ . + WatrCont)
You can also see if some of the included variables should be dropped:
drop1(m0, test=perm)
The usage of add1.cca is explained on its help page (see ?add1.cca).
Cheers, Jari Oksanen
the scores are orthogonal:
crossprod(pc$x)
or the off-diagonal elements are numerically zero, but they are
correlated:
cor(pc$x)
The only requirement we have is orthogonality, and uncorrelatedness is
a collateral damage in centred analysis.
Cheers, Jari Oksanen
See the following example
instead of
their sum, you can use argument add=TRUE for the second variable
(defaults FALSE) and ordisurf() overlays the fitted surface in an
existing plot.
Cheers, Jari Oksanen
--
Jari Oksanen [EMAIL PROTECTED]
__
R-help@r-project.org mailing list
https
today, and the new version already is available as a
source and Windows binary in the main CRAN home. With our faster
release cycles this will be in CRAN rather soon, and it is immediately
(or from our morning and Canada's late night) in packages at R-Forge.
Best wishes, Jari Oksanen
physically
equal dimensions. The mar/mai ratio or cra does not change with
device width height, so you must change those so that for fig looks
like it should.
I have no ideas if this works, but I think this still is your problem...
Greetings to the Moderator,
Jari Oksanen
Cheers, Jari Oksanen
Jari Oksanen jari.oksanen at oulu.fi writes:
Marc Moragues Marc.Moragues at scri.ac.uk writes:
Hi,
I am trying to calculate a distance matrix on a binary data frame using
dist.binary() {ade4}. This is the code I run and the error I get:
sjlc.dist - dist.binary(as.data.frame
in capitula, and the things called 'petals' in
documentation are ligulate, sterile ray-florets (each with vestigial petals
which are not easily visible in sunflower, but in some other species you may see
three (occasionally two) teeth).
cheers, jari oksanen
).
cheers, jari oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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.
it).
Cheers, jari oksanen
__
R-help@r-project.org mailing list
https://stat.ethz.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.
). Try
changing your data sets into regular R dist objects, and plot these
against each other (and as.dist really seems to work to data frames
directly):
plot(as.dist(d1), as.dist(d2))
This was only guessing, since the message did not contain sufficient
information.
cheers, jari oksanen
88 matches
Mail list logo