Re: [R] RDA Triplot

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

Re: [R] reliability of R-Forge?

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

Re: [R] lost in vegan package

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

Re: [R] lost in vegan package

-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.

Re: [R] step

, 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.

Re: [R] partial dbRDA or CCA with two distance objects in Vegan.

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

Re: [R] conditioning variables in dbRDA

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

Re: [R] metaMDS NMDS: use of alternative distances?

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

Re: [R] why is adnonis function called adonis {packageveg an}

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

Re: [R] Best subset of models for glm.nb()

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

Re: [R] cca standard error species

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()

Re: [R] Doubt about CCA and PCA

, 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

Re: [R] which to trust...princomp() or prcomp() or neither?

() 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

Re: [R] center of cluster of points in PCA

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

Re: [R] hvcluster() with distance method from vegdist(), package = vegan

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

[R] Plotting two distance matrices

). 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

Re: [R] Canberra distance

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.

[R] png() and pdf() alignment problems

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

Re: [R] adonis (vegan package) and subsetted factors

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

Re: [R] CPCA?

). 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.

Re: [R] Scatterplot Showing All Points

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

Re: [R] Error on distance matrix

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

Re: [R] CCA - manual selection

) 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

Re: [R] how to calcualte Jaccard Coefficient

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

Re: [R] Kruskal's MDS results

(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

Re: [R] Kruskal's MDS results

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

Re: [R] Re : PCA and automatic determination of the number of components

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

Re: [R] gam and ordination (vegan and labdsv surf and ordisurf)

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

Re: [R] prcomp(X,center=F) ??

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

Re: [R] Principle components analysis on a large dataset

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

Re: [R] Ellipse: Major Axis Minor Axis

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

Re: [R] biplot graphical options?

. 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.

Re: [R] How can I change characteristics of a cca biplot in R

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

Re: [R] NA in cca (vegan)

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

Re: [R] Mantel test least square line

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

Re: [R] Ellipse: Major Axis Minor Axis

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

Re: [R] (no subject)

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

Re: [R] Customizing ordination plots using symbols for factors

$feeding), col = as.numeric(FD.mat$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

Re: [R] Biplot for PCA using labdsv package

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

Re: [R] matrix correlations with different packages

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

Re: [R] Plotting MDS (multidimensional scaling)

. 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

Re: [R] NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity

. 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

Re: [R] envfit vector labels with ordiplot3d

(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

Re: [R] Envfit, inconsistant result?

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

Re: [R] Vegan: Anova.CCA accessing original data using option by=

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

Re: [R] Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC

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

Re: [R] ordination in vegan: what does downweight() do?

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.

Re: [R] any DCCA function in R?

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

Re: [R] Vegan(ordistep) error: Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed

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

Re: [R] Vegan(ordistep) error: Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed

. 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

Re: [R] Extracting part of anova.cca()

(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

Re: [R] Null models of species co-occurrence

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

Re: [R] identical function names from 2 packages

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

Re: [R] In vegan package: running adonis (or similar) on a distance matrix

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

Re: [R] metaMDS with large dataset produces 'insufficient data' warning

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

Re: [R] X-axis in meandist {vegan}

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

Re: [R] error of betadiver in vegan

) 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

Re: [R] vegan capscale 'subscript out of bounds' error

' 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

Re: [R] metaMDS in vegan: zero stress

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

Re: [R] dist like function but where you can configure the method

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

Re: [R] dist like function but where you can configure the method

:::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

Re: [R] varpart

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

Re: [R] Subsampling out of site*abundance matrix

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

Re: [R] Flipping axis 1 in CCA plot - vegan

. 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

Re: [R] Dependency on R-Forge Package

) 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

Re: [R] Species accumulation curves with differential sampling effort

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

Re: [R] species projected in a ordiplot

. 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

Re: [R] vegan CCA I am Completely new to ordination analyses

. 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

Re: [R] fisher.alpha warnings

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

Re: [R] Conditional CCA and Monte Carlo - Help!

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

Re: [R] Ordination Plotting: Warning: Species scores not available

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

Re: [R] rda variance partioning in vegan problems

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

Re: [R] vegan -varpart is bigger than 100% in total?

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

Re: [R] Vegan problem

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

Re: [R] BIOENV

(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

Re: [R] [R-sig-eco] reception of (Vegan) envfit analysis by manuscript reviewers

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

Re: [R] envfit output (vegan package) - not sure what it means

, 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

Re: [R] Efficient way to convert covariance to Euclidian distance matrix

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

Re: [R] Multivariate dispersion distances

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

Re: [R] What is the formula of Pseudo-F statistic in capscale in vegan?

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

Re: [R] Results from Vegan metaMDS varry depending on set.seed

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

Re: [R] Problem with metaMDS in vegan

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

Re: [R] problem with vegan function rda()

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

Re: [R] species names on a RDA plot

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

Re: [R] monte carlo simulations in permanova in vegan package

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 _

Re: [R] Vegemite Function is Cowardly refusing

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

Re: [R] Help with RDA analysis, function ''varpart'' in vegan

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

Re: [R] nMDS with R: missing values

-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