Howdy,
TWINSPAN is not in CRAN. It seems that you found it in github.
TWINSPAN is an old method, and it seems that people are forgetting how it
works. Here some narrative:
First, you have defined cut levels to transform your abundance data into binary
indicator “pseudospecies”. You give
e is no need to think it as an ordination.
Cheers, Jari Oksanen
On 7 Nov 2019, at 22:02, Couch, Claire Elizabeth
mailto:cou...@oregonstate.edu>> wrote:
I am analyzing some microbiome data by using unconstrained ordination (PCA
or NMDS) followed by environmental vector fitting with t
of ?printCoefmat which explains the usage of
stars.
Cheers, Jari Oksanen
> On 25 Sep 2019, at 20:51, melissa schindler
> wrote:
>
> Hello all,
>
> I have run a redundancy analysis on Hellinger transformed species abundance
> data and environmental variables.
>
> Onc
Yes, it is possible, and always has been when I have checked (which is not a
proof). You can check this by seeing that it has no negative eigenvalues in
principal coordinates analysis (apart from occasional negative almost-zero).
Legendre & Legendre book discuss this.
Cheers, Jari Oks
/vegan/.
cheers, Jari Oksanen
On 11 Jan 2019, at 20:09, Charlotte Reemts
mailto:cree...@tnc.org>> wrote:
I am using EcoTest.sample (rareNMtests package) to compare rarefaction curves
for 19 vegetation plots on two soil types (alluvial and canyon). The code below
produces the following warning
rowhouse, data =
metadata_fungi_out, permutations = , by = "margin")
Df SumOfSqs R2 F Pr(>F)
Stage:Growhouse 3 1.0812 0.23075 1.9998 0.006 **
Residual20 3.6045 0.76925
Total 23 4.6857 1.0
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01
9 2.7060 0.10408 0.0247 *
> Growhouse10.3765 0.37647 2.0889 0.08034 0.0542 .
> Stage:Growhouse 10.2171 0.21708 1.2045 0.04633 0.2507
> Residuals 20 3.6045 0.18023 0.76925
> Total 234.6857 1.0
> ---
> Sign
these tests were
implemented, but you may do that in your leisure if you think this is what you
want to have.
Cheers, Jari Oksanen
> On 16 Oct 2018, at 14:53 pm, Ellen Pape wrote:
>
> Hi,
>
> I know that A*B = A+B+A:B, but in this case, i.e. doing an adonis2 and
> sp
ction alone.
> ~A*B unfolds to ~A+B+A:B
Well, it was correct: the only **marginal** effect in ~A+B+A:B is A:B (A
and B are not marginal), and by = "margin" will only analyse marginal
effects.
Cheers, Jari Oksanen
>
> On Tue, 16 Oct 2018 at 11:51, Ellen Pape wrote:
>
>
them: it’s all up to your
responsibility.
cheers, Jari Oksanen
> On 14 Oct 2018, at 19:07 pm, Irene Adamo wrote:
>
> Dear all,
> I would like to create a distance matrix based on the similarity
> Chao-Jaccard index based on raw abundances in R but so far I have not been
> able
umentation (?metaMDS).
Have you worked like suggested in that document? What failed when you followed
the instructions?
Cheers, Jari Oksanen
From: R-sig-ecology <r-sig-ecology-boun...@r-project.org> on behalf of Chitra
Baniya <cbban...@gmail.com&
. Contributions are welcome at http://github.com/vegandevs/vegan.
cheers, Jari Oksanen
From: R-sig-ecology <r-sig-ecology-boun...@r-project.org> on behalf of Andrew
Halford <andrew.half...@gmail.com>
Sent: 08 February 2017 10:14
To: r-sig-ecology@r-project
one of the dummy
variables, R will do it for you and tell that some of your original variables
were aliased. This will not influence the results, though.
In conclusion: everything goes, but it is best to use the R way and define your
factor as a single factor.
Cheers, Jari Oksanen
> On 7
Ansley, I think you may have an old version of clustsig: the current one should
not give an error of missing undef.zero. Please check if you need to update.
cheers, j.o.
> On 7 Oct 2016, at 19:21 pm, Sarah Goslee wrote:
>
> I can't duplicate your error. Assuming the
hink about it.
Cheers, Jari Oksanen
From: R-sig-ecology <r-sig-ecology-boun...@r-project.org> on behalf of Ansley
Silva <daily.p...@gmail.com>
Sent: 04 August 2016 23:30
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] raremax value >2, can
Ewan,
You already got some good hints from Peter Michin (outside this list), but here
some comments.
> On 2 May 2016, at 20:22 pm, Ewan Isherwood <ewan.isherw...@gmail.com> wrote:
>
> Hi r-sig-ecology!
>
> This is mostly a message for Jari Oksanen or another Vegan
se of the Michaelis-Menten equation”. Michaelis-Menten is
available in fitspecaccum() in vegan.
Cheers, Jari Oksanen
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parallel to the axes) is good and you have an indicator variable for that, you
can use MDSrotate() function in vegan to rotate your solution to that direction
and then take that rotated axis as your explanatory variable.
HTH, Jari Oksanen
> On 11 Jan 2016, at 10:38 am, Martin Weiser &l
> On 11 Jan 2016, at 14:13 pm, Bob O'Hara wrote:
>
>
> Whilst I'm filling bandwidth, I'm not sure Jari's suggestion that you need
> the interaction term is correct. If a model is linear in axis1 and axis2,
> then any rotation is also linear, i.e. the transformation is
to
> use only first few axes of metric ordination instead of raw data: no
> ecological relevant information is lost, only the 'noise' is reduced.
>
> Best wishes
>
> Zoltan
>
> 2016.01.11. 11:11 keltezéssel, Jari Oksanen írta:
>> Contrary to common misbelief, NMDS ordina
the names may
be used loosely. There is also Horn index that is not implemented in
vegan::vegdist. For these indices, vegan follows Krebs’s “Ecological
Methodology”.
cheers, Jari Oksanen
> On 27 Nov 2015, at 15:41 pm, Zoltan Botta-Dukat
> <botta-dukat.zol...@okologia.mta.hu> wrot
think you need to have several data frames
for the data= argument, please consider cbind().
cheers, Jari Oksanen
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ernally turn it into dissimilarities using specified distance= method
(defaults “euclidean”). You should verify that the selected distance= method is
the one you need. The variables on the right-hand-side of the formula must be
in “raw” (observations times variables) format. They cannot be dista
Probaby the difference is the adjustment: varpart() uses adjusted R-squared,
but rda() output reports unadjusted proportions. RsqureAdj() function gives
both.
Cheers, jari Oksanen
From: R-sig-ecology <r-sig-ecology-boun...@r-project.org> on behalf
volume.ellipsoid function to find the volume. Obviously, these work in 2D.
Cheers, Jari Oksanen
> On 30 Sep 2015, at 17:38 pm, Baldwin, Jim -FS <jbald...@fs.fed.us> wrote:
>
> One metric for an "average width" that would be quick to calculate might be
> the diameter o
Natalie Zoltan,
I'd be more worried about the effect of outliers on the area of convex hulls.
Here an _ad hoc_ definition of outlier: outlier a single point that has a huge
effect on the area of an enclosing convex hull.
That said, two points are certainly on a line, and three points can be
-metric transformation is made to optimize the
goodness of fit to Euclidean ordination space.
Cheers, Jari Oksanen
On 16/07/2015, at 22:19 PM, Kate Boersma wrote:
Hi all.
I have a methodological question regarding non-metric multidimensional
scaling. This is not specific to R. Feel free
also adds
similar slope calculations for analytic species accumulation models (exact,
rarefaction, coleman) plus all non-linear regression models in
fitspecaccum() (function specslope()).
Cheers, Jari Oksanen
On 11/05/2015, at 12:09 PM, Jari Oksanen wrote:
Basic algebrra seems to lead
,], 126) # 19.47011
b - rarederatk(mite[1,], 126) # derivetive 0.04032 (with warnings)
abline(y-126*b, b) # matches the rarecurve plot
Cheers, Jari Oksanen
From: R-sig-ecology r-sig-ecology-boun...@r-project.org on behalf of Zoltan
Botta-Dukat botta
, it will be merged and included in the next
vegan release.
Thanks for reporting this.
Best wishes, Jari Oksanen
From: R-sig-ecology r-sig-ecology-boun...@r-project.org on behalf of
Christoph Eberhard Freiherr von Redwitz christoph.redw...@uni-rostock.de
Sent: 05 March
Alex,
It is possible that the documentation in vegan answers this. You can try
vegandocs(decision) and go to chapter Scaling in redundancy analysis that
also applies to capscale results.
Cheers, Jari Oksanen
From: R-sig-ecology r-sig-ecology-boun...@r
want to get summaries, check function meandist in vegan.
Cheers, Jari Oksanen
On 13/12/2014, at 02:17 AM, Kate Boersma wrote:
Hi all.
I have a community analysis data manipulation puzzle for you... hopefully
someone can help. Please let me know if this question needs clarification,
has
Negative values of what? If it is AIC, it is not a problem. With AIC, only
differences are meaningful. The observed values can be negative.
Cheers, Jari Oksanen
Sent from my iPad
On 29.11.2014, at 19.56, Manoeli Lupatini mlupat...@gmail.com wrote:
Dear all,
I am working with radfit
, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org r-sig-ecology-boun...@r-project.org
on behalf of Rich Shepard rshep...@appl-ecosys.com
Sent: 21 November 2014 00:08
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] Minimum Number of Observations
have
a certain number of animals, but their number is reduced with age so that you
have a kind of censored data (animals not available in all cases). Perhaps
somebody can propose a better analysis for such a censored data, if it is like
that.
Cheers, Jari Oksanen
On 24/10/2014, at 10:41 AM
several observations. That is true: then you can
proceed, but consult a statistician on the way to proceed.
Cheers, Jari Oksanen
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again in R-Forge, and has been
for a week, so that this is not the most recent and stable version of R-Forge,
but it is mostly safe.)
Cheers, Jari Oksanen
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exciting for the general public. You may consider contacting the package
maintainers directly.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org r-sig-ecology-boun...@r-project.org
on behalf of Tim Richter-Heitmann trich...@uni-bremen.de
.
I'm not convinced that it's a good idea, but I worked with someone who
needed it to fulfil contract obligations so I wrote it.
It looks like a very good idea to me.
Cheers, Jari Oksanen
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that may work even with the current code: check Legendre Legendre
latest edition.
Cheers, Jari Oksanen
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in these
data: you run out of degrees of freedom.
Sorry for top-posting and bad formatting: this MS Outlook.
cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org r-sig-ecology-boun...@r-project.org
on behalf of Simone Ruzza simone.ruzz
. I have tried to spell
out that warning in vegan manual pages, but people seem to ignore those parts
of the text.
cheers, Jari Oksanen
On 28/05/2014, at 20:05 PM, Nicholas J. Negovetich wrote:
I have a question related to rarefaction of our samples. Unlike all of the
examples of which I'm
Dear Claire Della Vedova,
It seems that you have searched in many places, except in vegan documentation.
Look at the vignette on Design decisions, section Scaling in redundancy
analysis.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org r
of M variables
really are independent. However, this really needs to be taken into account if
M is low. I have no idea how is that in your case.
Cheers, Jari Oksanen
On 13/05/2014, at 15:32 PM, Zbigniew Ziembik wrote:
I am not sure, but it seems that your problem is related to
compositional
of M variables
really are independent. However, this really needs to be taken into account if
M is low. I have no idea how is that in your case.
Cheers, Jari Oksanen
On 13/05/2014, at 15:32 PM, Zbigniew Ziembik wrote:
I am not sure, but it seems that your problem is related to
compositional
within adonis code, and bootstrapping is certainly
better. What is sure is that the equations you gave in your message won't work.
I have never used these adonis coefficients, and I have no idea how to use
them, and therefore I don't have any opinion about their use.
Cheers, Jari Oksanen
On 09
Dear Tracy,
You can see if Helene Wagner's mso() in function in vegan satisfies your needs
for analysing spatial dependence. Reference and further description in ?mso.
Cheers, Jari Oksanen
On 02/04/2014, at 00:12 AM, Pinney, Tracy A wrote:
Hello List,
I have two questions.
1.)How
{}
for(i in 1:5) x[k==i,] - calibrate(rda(decostand(mite, hell) ~
SubsDens+WatrCont, mite.env, subset = k != i), newdata = decostand(mite[k==i,],
hell))
Easy, but not very good a prediction (cca would be marginally better, like it
usually is).
Cheers, Jari Oksanen
On 29/03/2014, at 04:44 AM
Patches welcome. It is best to use vegan in GitHub.
Pairwise tests are not high on my TODO list, because they are so much against
what I've learnt from statistical theory and I detest tests.
Cheers, Jari Oksanen
Sent from my iPad
On 27.3.2014, at 17.54, Gavin Simpson ucfa...@gmail.com wrote
Except that t-test does not assume that *observations* are normally
distributed, nor that variances are equal.
Avoid non-parametric tests: they assume too much of data properties.
For var.equal assumption in t.test, see ?t.test.
Cheers, Jari Oksanen
function
does not return information for getting residuals. Neither would they be
residuals in the traditional meaning of the word as we are dealing with
dissimilarities or distances, and these cannot be negative. We got to discuss
this with vegan developers.
Cheers, Jari Oksanen
an average of zero and some of which are negative).
Cheers, jari Oksanen
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details, this is a blind watchmaker recommendation.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r-project.org]
on behalf of Ivailo [ubuntero.9...@gmail.com]
Sent: 26 February 2014 16:23
To: Rajendra Mohan panda
Cc: r-sig
the
hydrobiological variables, is there any way or code in plot that also show
the names of zooplankton groups?
Dear Mahnaz Rabbaniha,
Have you tried plot(vare.cca, type=t)?
Cheers, Jari Oksanen
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must take into account the number of estimated
parameters that varies from zero to three.
Cheers, Jari Oksanen
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Function meandist() should do this. Its name is kind of hint.
Cheers, Jari Oksanen
On 16/12/2013, at 21:16 PM, Andres Mellado Diaz wrote:
Dear list memnbers,
I would greatly appreciate any suggestion on how to get averaged distance
values (and errors) between groups of samples using vegan
variables that are
neither numeric nor factors.
Cheers, Jari Oksanen
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. If there are some other problems, I want to fix them, too. Therefore I
really want to know what happened with your application. I try to reproduce
your problems, but this is kind of blind watchmaker's works as I don't have a
reproducible test case. Therefore I have to ask stubbornly.
Cheers, Jari
and a *reproducible*
example. We haven't got any now, and I cannot reproduce your problem.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r-project.org]
on behalf of Stephen Sefick [sas0...@auburn.edu]
Sent: 04 December 2013
It is easy if you have C and Fortran compilers plus unix tools. I assume most
people do not have those. Then 'easy' is quite different a concept.
Cheers, Jari Oksanen
alkuperäinen viesti
Lähettäjä: Hadley Wickham
Lähetetty: 05.12.2013, 16:19
Vastaanottaja: Eduard Szöcs
Kopio: r-sig
higher R2 than
dist(y) ~ dist([x1,x2]) -- bioenv is based on this.
Cheers, Jari Oksanen
Sent from my iPad
On 4.12.2013, at 20.19, Sarah Goslee sarah.gos...@gmail.com wrote:
Hi,
That seems a bit odd: can you provide a reproducible example, off-list
if necessary?
Sarah
On Wed
species. You can supply the original community
data (which has the information on species) as argument 'comm' in capscale().
Cheers, Jari Oksanen
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. Since the alternatives
are provided, you can study the issue independently.
The existence of a method is not a sufficient reason to use that method.
Cheers, Jari Oksanen
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in this dune example: RMSE is larger than standard deviation of A1 (but you
could almost guess this by looking at the low constrained eigenvalues of the
model).
The code above uses the 'subset' argument of vegan::rda and the subset()
function of R to make the code a bit easier to write.
Cheers, Jari
If you use these, remember that R cos() needs argument in radians.
Cheers, Jari Oksanen
Sent from my iPad
On 18.10.2013, at 8.40, Ivailo ubuntero.9...@gmail.com wrote:
On Fri, Oct 18, 2013 at 6:16 AM, Michael Marsh sw...@blarg.net wrote:
If you want a measure of exposure, i. e., heat, I
it break by returning several values
instead of one?
If you want to have this, you really do not need to use vegan.
vegan:::RsquareAdj.lm() takes its results from summary(lm_object). You can
use that stats:::summary.lm directly.
Cheers, Jari Oksanen
. If
you really *know* that you need non-centred RDA. then you know how to change
those lines of code in rda.default.
Cheers, Jari Oksanen
From: Paolo Piras [paolo.pi...@uniroma3.it]
Sent: 03 October 2013 15:52
To: Jari Oksanen; r-sig-ecology@r-project.org
to to specify a quantitative null model. Both null models and
oecosimu are completely re-written and re-designed in development versions.
Cheers, Jari Oksanen
On 25/09/2013, at 15:56 PM, v_coudr...@voila.fr
wrote:
Thank you very much. Yes it is working with oecosimu, exept that it does not
seem to work
for.
Cheers, Jari Oksanen
alkuperäinen viesti
Lähettäjä: Mitchell, Kendra
Lähetetty: 31.07.2013, 02:38
Vastaanottaja: r-sig-ecology@r-project.org r-sig-ecology@r-project.org
Aihe: [R-sig-eco] subsetting lower triangle distance matrix based on variable
in another object
I have a number
need scaling to see
shades of colours. Names can also be unreadable in large tables. Fixes are
welcome. I think ade4 may have something similar.
Cheers, Jari Oksanen
alkuperäinen viesti
Lähettäjä: Basil Iannone
Lähetetty: 24.07.2013, 14:57
Vastaanottaja: Sarah Goslee
Kopio: r-sig
In some cases lousy email system mandates promoting piracy: i replys, the
previous messages are treated as appendices that cannot be edited. This also
means that you must top-post. Kudos goes to MicroSoft + Nokia.
Cheers, Jari Oksanen
alkuperäinen viesti
Lähettäjä: THIOULOUSE JEAN
).
Cheers, Jari Oksanen
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.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
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, Jari Oksanen
So, I am thinking that examining the relationship between the microbial
community and this subset of environmental variables might not be possible
without my first manually curating which samples and variables should be
included, correct?
Thank you,
Colleen
--
View
On 01/06/2013, at 05:20 AM, Jari Oksanen wrote:
The CCA seems to run just fine, but when I attempt to do the posthoc tests
such as anova.cca (anova(toolik250.cca,by='terms',perm=999), I get an error
message: Error in anova.ccabyterm(object, step = step, ...) : number of
rows has changed
of missing
values, nothing may be very reliable. It could be possible to collect together
and combine permutation test results after multiple imputation, but better
consult a statistician before trying to do this.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
Fernando,
For background reading you may check
Stevens. M.H.H. (2009) A Primer of Ecology with R. Use R! Series. Springer.
and associated 'primer' package in CRAN. The book discusses functional
responses.
Cheers, Jari Oksanen
From: r-sig-ecology-boun
of
doing the same. For instance, you seem to want to have sum contrasts, but with
different baseline level. Check functions like model.matrix, contrasts,
relevel, and as.data.frame. However, the magnitude of coefficient also depends
on specific contrasts that you use.
Cheers, Jari Oksanen
'. The designdist() function calculates (dis)similarities between rows.
You must transpose (t()) your data if you want to have dissimilarities between
columns. The code is pure R so that you can see how to do these calculations
yourself.
Cheers, Jari Oksanen
for the following data:
ST01 ST02
the very beginning. That is, form 1960s.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r-project.org]
on behalf of Erin Nuccio [enuc...@gmail.com]
Sent: 24 April 2013 12:30
To: r-sig-ecology@r-project.org
Subject: [R
'
argument in metaMDS to trigger step across dissimilarities. We claim that this
rarely necessary with the monoMDS engine we use currently, but sometimes it is
needed.
Without hands on your data it is difficult to guess more.
Cheers, Jari Oksanen
Sent from my iPad
On 22.4.2013, at 22.31
* ordination to any
dissimilarity measure. So NMDS finds metric solution from any dissimilarity
measure.
I
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
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))
and it is really useful to validate the results...
Cheers, Jari Oksanen (Finland)
-Oorspronkelijk bericht-
Van: r-sig-ecology-boun...@r-project.org
[mailto:r-sig-ecology-boun...@r-project.org] Namens Mauricio
Zambrano-Bigiarini
Verzonden: mercredi 20 mars 2013 09:29
Aan: r-sig
class(d) say. If says dist (possibly
with some other alternatives), you are safe. If your 'd' are not of class
dist, you can try if as.dist(d) changes them to dist.
Cheers, Jari Oksanen
From: r-sig-ecology-boun...@r-project.org [r-sig-ecology-boun...@r
from R-Forge, or you can install devel
version of vegan with
install.packages(vegan, repos=http://r-forge.r-project.org;)
It will take a day at minimum to get the version packaged in R-Forge.
Cheers, Jari Oksanen
On 26 Feb 2013, at 3:49, Sarah Loboda wrote:
Hi,
Here's the reproducible example
Kay,
This should not work if the function is correctly written. You say that the
terms in your formula are in data=env, but there are no variables env$NFac and
env$Fac in env -- but there are NFac and Fac.
Cheers, Jari
Sent from my iPad
On 23.2.2013, at 12.15, Kay Cichini
, and this will give some examples of
defining restricted permutations. At some timeframe we are completely moving
to the permute package, but you can already use its permutation matrices as
input with these new and upcoming versions of vegan from R-Forge.
Cheers, Jari
--
Jari Oksanen, Dept Biology
like the
Andes.
Cheers, Jari Oksanen
On 12/02/2013, at 00:15 AM, Carolina Bello wrote:
Hi
I have some problems with the vegdist function.I want to do a hierarchical
cluster from 138037 pixels of 1 lkm^2 from a study area of colombian Andes.
I have distributions models for 89 species so i
effects.
You cannot expect lme4 extensions to formula to work in other packages. We can
parse many fixed effect formulae to a model matrix, but there is a long way of
getting permutations to work in some specific way for variables tagged as
random factors.
Cheers, Jari Oksanen
I'm analyzing
scores can be found from the result object (see
?cca.object), but scores() also scales results as requested (argument
'scaling').
HTH, オクサネ槍
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
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LINPACK = TRUE
option disappears within a few months.
Best wishes, Jari Oksanen
On Wed, Jan 16, 2013 at 11:35 AM, Gavin Simpson gavin.simp...@ucl.ac.uk
wrote:
Hi Jesse,
Can you send me the data *and* *exact* code you used so I can look into
this further? I promise to delete the data
there is a high number of methods you can apply, but why? What you
try to analyse? What are your questions?
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
'zerodist = add' is only necessary with MASS::isoMDS()
that is unable to handle zero distances.
We have changed the default of 'sfgrmin' in http://www.r-forge.r-project.org/
so that you should not see this problem in the next vegan releases.
Cheers, Jari Oksanen
On 05/12/2012, at 21:15 PM, Ewan
-915-5144
Phone - 662-915-1077
On 11/29/12 9:43 AM, Jari Oksanen jari.oksa...@oulu.fi wrote:
Steve,
This is R, so it is not about whether this can be done, but how this can
be done. Unfortunately, doing exactly this requires some fluency in R.
Doing something similar is very simple
think that the whole
idea of post hoc tests is weird, to put it mildly).
Cheers, Jari Oksanen
Sent from my iPad
On 25.11.2012, at 0.54, Andre Rovai asro...@gmail.com wrote:
Dear friends,
I have been recently introduced to R and am dedicating myself to go deeper
on it. It can be tricky
this R convention, but similarities are not R compliant.
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
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than 1000: you can get nicer round
figures. Once we were more patronizing and dropped one permutation if the user
asked for even hundred or thousand, but then we thought that this is up to user
to decide and none of our business.
Cheers, Jari Oksanen
On 27/08/2012, at 23:23 PM, Maurício Moraes
simple introductory example (like that in vegandocs(intro)). Of course,
there is PC-Ord...
Cheers, Jari Oksanen
## S3 method for class 'cca':
points(c1.rda, display = sites, choices = c(1, 2), scaling = 2,
arrow.mul, head.arrow = 0.05, select, const, ...)
## S3 method for class
and can't
check the web easily.
HTH, Jari Oksanen
alkuperäinen viesti
Lähettäjä: Gian Maria Niccolò Benucci
Lähetetty: 25.06.2012, 12:40
Vastaanottaja: r-sig-ecology@r-project.org
Aihe: [R-sig-eco] metaMDS - avoid species overlap in plots
Hi community,
Very simple question. How
. Does it help if you use
Model - cca(hs.spec ~ ., data = scale(hs.ev))
?
Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
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