### Re: [R-sig-eco] twinspan classification rules as narrative

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

### Re: [R-sig-eco] How to get the total variance explained from an envfit object?

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

### Re: [R-sig-eco] Vegan Function anova.cca: No Significance Codes Legend in Output

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

### Re: [R-sig-eco] transformation of Bray-Curtis in Euclidean

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

### Re: [R-sig-eco] standard deviation error for EcoTest.sample

/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

### Re: [R-sig-eco] 2-way adonis (PERMANOVA) incl interaction - how to test for main effects?

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

### Re: [R-sig-eco] 2-way adonis (PERMANOVA) incl interaction - how to test for main effects?

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

### Re: [R-sig-eco] 2-way adonis (PERMANOVA) incl interaction - how to test for main effects?

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

### Re: [R-sig-eco] 2-way adonis (PERMANOVA) incl interaction - how to test for main effects?

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: > >

### Re: [R-sig-eco] distance matrix with chao-jaccard method

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

### Re: [R-sig-eco] instability of NMDS

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&

### Re: [R-sig-eco] Factors in partial RDA part 2

. 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

### Re: [R-sig-eco] Factors in partialRDA

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

### Re: [R-sig-eco] Errors with Simprof for cluster significance

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 Gosleewrote: > > I can't duplicate your error. Assuming the

### Re: [R-sig-eco] raremax value >2, cannot run rarefy

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

### Re: [R-sig-eco] Follow-up to Vegan metaMDS: unusual first run stress values with large data set

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

### Re: [R-sig-eco] specaccum

se of the Michaelis-Menten equation”. Michaelis-Menten is available in fitspecaccum() in vegan. 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] NMDS axes scores

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

### Re: [R-sig-eco] NMDS axes scores

> On 11 Jan 2016, at 14:13 pm, Bob O'Harawrote: > > > 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

### Re: [R-sig-eco] NMDS axes scores

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

### Re: [R-sig-eco] Morisita horn similarity index

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

### Re: [R-sig-eco] RDA

think you need to have several data frames for the data= argument, please consider cbind(). 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] RDA

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

### Re: [R-sig-eco] Differences between total constrained inertia (rda) and variance explained (varpart()) in vegan

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

### Re: [R-sig-eco] Quantifying widths of polygons

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

### Re: [R-sig-eco] calculate dispersion index (betadisper, vegan)

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

### Re: [R-sig-eco] distances in NMDS ordination space

-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

### Re: [R-sig-eco] slope for rarefaction curve

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

### Re: [R-sig-eco] slope for rarefaction curve

,], 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

### Re: [R-sig-eco] vegan: goodness() and pRDA

, 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

### Re: [R-sig-eco] CAPSCALE plot output

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

### Re: [R-sig-eco] Community distance matrix deconstruction

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

### Re: [R-sig-eco] help radfit()

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

### Re: [R-sig-eco] Minimum Number of Observations for pcaCoDa?

, 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

### Re: [R-sig-eco] Logistic regression with 2 categorical predictors

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

### Re: [R-sig-eco] Regression with few observations per factor level

several observations. That is true: then you can proceed, but consult a statistician on the way to proceed. 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] SIMPER problem: invalid 'nrow' value (too large or NA)

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

### Re: [R-sig-eco] [vegan]Error in as.vector(x, mode) : , cannot coerce type 'builtin' to vector of type 'any' when perfroming a cca on a dataframe

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

### Re: [R-sig-eco] predict NMS scores for new samples

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

### Re: [R-sig-eco] adonis() and collinearity

that may work even with the current code: check Legendre Legendre latest edition. 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] simple question about CCA

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

### Re: [R-sig-eco] Manual Rarefaction and CI's

. 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

### Re: [R-sig-eco] how are compuetd the species scores of pca from veganpackage ?

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

### Re: [R-sig-eco] Measurement distance for proportion data

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

### Re: [R-sig-eco] Measurement distance for proportion data

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

### Re: [R-sig-eco] calculating standard error of coefficients from adonis model

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

### Re: [R-sig-eco] residuals in RDA, and test for spatial autocorrelation

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

### Re: [R-sig-eco] cross validation in CoCA and CCA

{} 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

### Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER

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

### Re: [R-sig-eco] report out by t.test

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

### Re: [R-sig-eco] Extract residuals from adonis function in vegan package

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

### Re: [R-sig-eco] Extract residuals from adonis function in vegan package

an average of zero and some of which are negative). 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 accommodate data with negative values for Canonical Correspondence Analysis in R using vegan Package

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

### Re: [R-sig-eco] cca

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

### Re: [R-sig-eco] Ranked abundance distribution

must take into account the number of estimated parameters that varies from zero to three. 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] Mean distance values (and errors) between groups of samples using vegan

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

### Re: [R-sig-eco] NA error in envfit

variables that are neither numeric nor factors. 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 error in envfit

. 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

### Re: [R-sig-eco] NA error in envfit

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

### Re: [R-sig-eco] NA error in envfit

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

### Re: [R-sig-eco] Community composition variance partitioning?

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

### Re: [R-sig-eco] NA in species scores using capscale in vegan

species. You can supply the original community data (which has the information on species) as argument 'comm' in capscale(). 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] Multivariate Analyses of Ecological Communities

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

### Re: [R-sig-eco] Cross validate model with calibrate

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

### Re: [R-sig-eco] angular statistics

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

### Re: [R-sig-eco] vegan RsquareAdj() for lm models

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

### Re: [R-sig-eco] vegan RsquareAdj() for lm models

. 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

### Re: [R-sig-eco] null model for testing nestedness

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

### Re: [R-sig-eco] subsetting lower triangle distance matrix based on variable in another object

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

### Re: [R-sig-eco] Heat Map for species - code from Numerical Ecology with R

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

### Re: [R-sig-eco] Heat Map for species - code from Numerical Ecology with R

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

### Re: [R-sig-eco] error in MetaMDS

). 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] forward selection RDA after controlling for constraints

. 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://stat.ethz.ch/mailman/listinfo/r-sig

### Re: [R-sig-eco] anova.cca question / missing data in constraining matrix

, 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

### Re: [R-sig-eco] anova.cca question / missing data in constraining matrix

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

### Re: [R-sig-eco] anova.cca question / missing data in constraining matrix

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

### Re: [R-sig-eco] Functional response type II question, curve fitting and

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

### Re: [R-sig-eco] adonis

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

### Re: [R-sig-eco] using Pearson's Chi-squared to verify dependence among species distribuion

'. 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

### Re: [R-sig-eco] envfit and NMDS

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

### Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf

' 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

### Re: [R-sig-eco] CCA vs NMDS and ordisurf

* 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 ___ R-sig-ecology

### Re: [R-sig-eco] Conversion of lat/long coordinates to ETRS89

)) 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

### Re: [R-sig-eco] nested.npmanova -- distance matrices as input?

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

### Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?

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

### Re: [R-sig-eco] Issue with BiodiversityR::nested.npmanova

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

### Re: [R-sig-eco] adonis and temporal changes

, 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

### Re: [R-sig-eco] Fwd: vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande

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

### Re: [R-sig-eco] Adonis and Random Effects

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

### Re: [R-sig-eco] Query as db-RDA

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

### Re: [R-sig-eco] Error in La.svd(x, nu, nv) : error code 1 from Lapack routine 'dgesdd'

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

### Re: [R-sig-eco] pca or nmds (with which normalization and distance ) for abundance 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

### Re: [R-sig-eco] Vegan metaMDS: unusual first run stress values with large data set

'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

### Re: [R-sig-eco] summing F stats and permutation

-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

### Re: [R-sig-eco] post-hoc test for adonis PERMANOVA

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

### Re: [R-sig-eco] ANOSIM

this R convention, but similarities are not R compliant. 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] Multivariate ANOVA based on dissimilarities

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

### Re: [R-sig-eco] IndVal groups Plotting an RDA with labels

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

### Re: [R-sig-eco] metaMDS - avoid species overlap in plots

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

### Re: [R-sig-eco] Retrieving canonical coefficients and correlation coefficients according to ter Braak using vegan package cca() function

. 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 ___ R-sig-ecology mailing