Re: [R-sig-eco] output from ordisurf

them to draw the surface with the contour() command. The grid item is available from vegan working version 1.16-3 (revision 532) in R-Forge, and Windows binary is available (probably) from tomorrow morning (Central European Standard Time). Best wishes, Jari Oksanen -- Jari Oksanen [EMAIL

Re: [R-sig-eco] Question on height for hclust function

effect on the scales. The choice of clustering method has a huge impact. cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Intepreting a plot from a constrained NMDS

(and go along the axes), then it would be meaningful to look a the relationship of axis and something else. And indeed, there is no constrained NMDS in vegan. It is unconstrained with an interpretation through vector fitting. cheers, jari oksanen Stephen Sefick On Sat, Dec 6, 2008 at 11:58 AM

Re: [R-sig-eco] Vegan DCCA axis length

in which Gavin Simpson and Jari Oksanen states that are not available routines in vegan to retrieve this information. I am interested in the length of the DCCA/pCCA axis as I would like to perform a similar analyses to the one Lancaster et al. 1996 performed to measure community persistence

Re: [R-sig-eco] Neighbor sampling is random?

E. C. Pielou may be one of the first who wrote about this. Check her book 'Mathematical ecology' (J. Wiley, 1977). Best wishes, Jari Oksanen -Original Message- From: Paulo Inácio de Knegt López de Prado Sent: 04.07.2009, 17:35 To: r-sig-ecology@r-project.org Subject: [R-sig-eco

Re: [R-sig-eco] wascores() for metaMDS?

that species are not points nor arrows. Vegan tutorial (from the Web) gives an example. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Fixing parameters in GLM and Mixed Effects Models

of the other parameters (c-g) turn out to be, as well as the model fit when using the forced parameters in conjunction with the free parameters. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-eco] Mantel test with skew-symmetric matrices?

On 1/10/09 20:36 PM, Sarah Goslee sarah.gos...@gmail.com wrote: I can only speak for the mantel() within ecodist, but I can tell you that it will not take full matrices - the upper triangle will be dropped. You could roll your own very easily, but it would be exceedingly slow, eg: mat1 -

Re: [R-sig-eco] trouble with BiodiversityR:diversityresult function

easily spot those changes (probably in BiodiversityRGUI, diversityresult, diversityresult0). I have cc'ed this to Roeland Kindt, but I think the Internet connection is not always so good so that it may take some time before he answers. I can look if I can hack around this in vegan. Cheers, Jari

Re: [R-sig-eco] trouble with BiodiversityR:diversityresult function

On 12/10/09 19:54 PM, Roman Luštrik roman.lust...@gmail.com wrote: Hello list, I have a felling this is a generic error but nonetheless, it has been bugging me extensively. If anyone can chip in, I would most appreciate. I'm trying to calculate expected species richness, following

Re: [R-sig-eco] using two distance metrices in formula

tests available in several packages in R, but what are the things you want to solve by using dissimilarities? Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] using two distance metrices in formula

their conflicting arguments make sense, they are not yet an optimal solution. Cheers, Jari Oksanen so we thought it would be a good idea not to use mantel and friends since the problem of IBD seems to need a different approach here. best, Jens Sarah Goslee schrieb: That doesn't make much

Re: [R-sig-eco] Rotations for PCoA?

. They are not the same as the strict rotation scores for factors in Gower metric (but should be the same as the Legendre scores for continuous variables), but may be more intuitive. Cheers, jari oksanen ___ R-sig-ecology mailing list R-sig-ecology@r

Re: [R-sig-eco] how to calculate axis variance in metaMDS, pakage vegan?

print.wcmdscale!) NMDS is really intended for nonlinear mapping onto *low* number of dimensions. Cheers, Jari Oksanen NMS.trial Call: metaMDS(comm = sqrtABCD, distance = bray, k = 23, trymax = 100, autotransform = F) Nonmetric Multidimensional Scaling using isoMDS (MASS package) Data

Re: [R-sig-eco] how to calculate axis variance in metaMDS, pakage vegan?

this: stress 11.6 is really fine. I think that if you get stress down to 5% (0.05) or less, then there is something fishy in your data or in your model specification, like overfitting. Cheers, Jari Oksanen But, of course, our goal is to reduce the observed complexity of nature

Re: [R-sig-eco] capscale() for PCoA-CDA

On 3/12/09 23:54 PM, gabriel singer gabriel.sin...@univie.ac.at wrote: Hi everybody, Anybody has used capscale() in package vegan to compute a PCoA-CDA as suggested by Anderson and Willis 2003 (Ecology 84: 511 ff) using one or more factors as predictors? Then I wonder about: *) How to

Re: [R-sig-eco] Fwd: Fwd: how to calculate axis variance in metaMDS, pakage vegan?

for mixed models in any other vegan function. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] dissimilarity and species turnover

if you are serious), dig up the late 2008 issue of the Ecology with the Legendre mates vs. Tuomisto discussion -- somewhere around pages 3230 to 3256 of vol 89). That's for the starter. Cheers, Jari Oksanen I've been exploring using this approach for a similar problem. I'd be curious to know

Re: [R-sig-eco] vegan package: goodness.cca function? (citations needed)

(CCA) model after using the function goodness.cca in vegan. In his explanation of the diagnostic tools for CCA (http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/goodness.cca.html), Jari Oksanen states that It is a common practise to use goodness statistics to remove species from ordination

Re: [R-sig-eco] anosim, mrpp and adonis

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 ___ R-sig-ecology

Re: [R-sig-eco] add lines outside of the plot region

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

Re: [R-sig-eco] null models with continuous abundance data

. 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

Re: [R-sig-eco] null models with continuous abundance data

(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

Re: [R-sig-eco] ordiplot3d

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

Re: [R-sig-eco] ordiplot3d

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

Re: [R-sig-eco] nmds in 3D

sets have 2.5 dimensions (Kruskal). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] na.exclude in vegan

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 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-eco] NMDS Usage

. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] How to calculate a community similarity index not supported by vegan

, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] vegdist producing empty result object

-emptiness. You have other tools for this, like looking at the object (or writing a query to a mailing list). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Two questions about vegan

the error message you got from scale.default. HTH, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Data transformation prior to RDA

, but there is an improved way. Check ordistep() for Canoco-style analysis, and add1.cca, drop1.cca for another ways. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] adonis and contrasts

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

Re: [R-sig-eco] change arrow colour when plotting rda

arrows and labels, and points() only unlabelled arrows. See ?text.cca, ?points.cca for details and further arguments. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Graphical parameters in metaMDS

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

Re: [R-sig-eco] nmds -- Error in class(S) ..., package conflict between vegan and ??

() 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

Re: [R-sig-eco] Vegan fisher.alpha error

? Cheers, jari oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Distance matrix based on correlation coefficient

seems not to work. 1 - cor(dat) ## dissimilarity Actually the canonical transformation to distance is sqrt(2-2*cor(dat)). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-eco] Negative Data Error with Decorana in Vegan

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

Re: [R-sig-eco] Species fit in ordination

in selecting the species to display? I will be very grateful for any help. HTH, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] adonis and model selection

: update(m, . ~ . - Use) As usual, contributions are welcome. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] negative F value in adonis()

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

Re: [R-sig-eco] pearson correlation with axes of NMDS or capscale

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

Re: [R-sig-eco] Warnings with Vegan radfit command

the warning. That's life, but no reason to worry. You can see this by looking and plotting the results. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Warnings with Vegan radfit command

, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] hurdle model

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 ___ R-sig-ecology mailing list R-sig-ecology@r

Re: [R-sig-eco] Making this plot in R: relative abundance vs. environmental gradient with each species ranked by niche optimum

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 ___ R-sig

Re: [R-sig-eco] specifying a chord distance matrix in metaMDS

zero columns (any(colSums(tmp) = 0)). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Using pcnm to correct for spatial autocorrelation

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

Re: [R-sig-eco] ANOSIM in vegan

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

Re: [R-sig-eco] Quantifying functional trait diversity through Gowerdistance and pcoa

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 ___ R-sig

Re: [R-sig-eco] relative compositional dissimilarity among sites against a continuous variable

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

Re: [R-sig-eco] relative compositional dissimilarity among sites against a continuous variable

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

Re: [R-sig-eco] relative compositional dissimilarity among sites against a continuous variable

was your problem, so we have no idea if you had a meaningful analysis. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] parametric estimators for species richness in R

). Therefore I'd like to think a bit before I release these functions: there is a danger people may use them... Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Capscale: Centroids ignored with Condition() in formula

(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

Re: [R-sig-eco] Displaying estimators from specpool or estimateR

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

Re: [R-sig-eco] permutest.cca and means seperation?

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 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org

Re: [R-sig-eco] Displaying estimators from specpool or estimateR

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

Re: [R-sig-eco] Displaying estimators from specpool or estimateR

, 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 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch

Re: [R-sig-eco] save graphics as tiff

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

Re: [R-sig-eco] Can Gravy's HOF Ignore NAs?

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

Re: [R-sig-eco] null models for a single species

permutation. I have no idea of your hypothesis, though, and I can't help here. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] metaMDS vs. isoMDS for NMDS

, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Change in rotated NMDS scores as a response variable

, 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

Re: [R-sig-eco] adonis with continuous variables

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

Re: [R-sig-eco] stratifying variables in Adonis

, 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 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https

Re: [R-sig-eco] Error with raup distance in metaMDS

not occur in your data) will influence your data. That is only informational, and not an error. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Sites names with spaces in ordiplot

' as you can see if you read the help page ?metaMDS (which may not be a bad idea). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] BVSTEP (PRIMER package) rutine in R

out how to perform a BVSTEP, So what is BVSTEP? Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] labels to a varpart diagram

haven't done that yet (contributions are welcome and will be credited in the documentation). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] The TWINSPAN program

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 ___ R-sig

Re: [R-sig-eco] The final result of TWINSPAN

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

Re: [R-sig-eco] passive projection of species richness

?envfit, ?ordisurf. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] vegan RDA triplot species arrows

. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] How to decrease inflation factor of environmental variables in CCA.

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 ___ R-sig-ecology mailing

Re: [R-sig-eco] vegan RDA triplot species arrows

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

Re: [R-sig-eco] Cluster Analysis

. 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

Re: [R-sig-eco] Anderson and Willis 2003, CAP squared canonical correlations of delta^2

^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

Re: [R-sig-eco] PCA with vegan

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 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-eco] pDCA

). Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] vegan Mantel test

in which case it is outside 95% of the permuted values? Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] envfit and adonis restricted permutations

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 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch

Re: [R-sig-eco] standard variation in dissimilarity matrix

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 ___ R-sig-ecology mailing list R-sig-ecology@r

Re: [R-sig-eco] RDA vegan: correlation coefficient among environment variables, species axes and environmental axes results

(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 ___ R-sig-ecology mailing

Re: [R-sig-eco] Envfit function

- metaMDS(bryceveg) ordisurf(m ~ slope, brycesite, knots=1, bubble=4) plot(envfit(m ~ slope, brycesite)) Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] vegan rda

? 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

Re: [R-sig-eco] Help PCNM analysis

] 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

Re: [R-sig-eco] NMDS trajectory plots

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 ___ R-sig-ecology mailing list R-sig-ecology@r

Re: [R-sig-eco] interpreting adonis results

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

Re: [R-sig-eco] MANCOVA in R

(). 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

Re: [R-sig-eco] MANCOVA in R

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

Re: [R-sig-eco] Fitting growth curve in a species accumulation curve (SAC)

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

Re: [R-sig-eco] The problems on BIO-ENV procedure by [R]

(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 ___ R-sig

Re: [R-sig-eco] order of explanatory variables in vegan CCA

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

Re: [R-sig-eco] vegan::adonis, SS, order of terms

this disagree with your reading? Cheers, Jari Oksanen -- Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] singletons and doubletons in vegan

want to have something more? Cheers, Jari Oksanen -- Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https

Re: [R-sig-eco] Is adonis the right test for me?

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

Re: [R-sig-eco] Error in CAPdiscrim() in BiodiversityR

-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

Re: [R-sig-eco] Error in CAPdiscrim() in BiodiversityR

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

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