[R-sig-eco] betadisper - distance form centroids

Hello community, I have a silly question about betadisper() output interpretation. I am using the function betadisper() after adonis to test for homogeneity of variances. I have used it a lot in the years but I never get to look at the boxplots output with the necessary attention.

Re: [R-sig-eco] Question about Eveness value comparison

Hello Luis, I suggest you to try the vegan and BiodiversityR packages. Best, Gian On Sat, 12 Dec 2020 at 02:03, Luis Fernando García wrote: > Dear all, > > I am wanting to compare the Eveness value in four localities. I found the > sbdiv function in the simboot package which makes exactly

[R-sig-eco] interaction effect in capscale, how to calculate

Hello sig-r-eco community, I would love to have some insights on my interpretation of capscale() and how to assess the variance explained by the interaction effect. Imagine a model like this: Var1 + Var2 + Var1:Var2 > RsquareAdj(capscale(otu_table ~ Var1 + Var2 + Var1:Var2, metadata, distance =

Re: [R-sig-eco] reorder vegdist objects

ot a statistician but software developer... hope that other members > > of the mailing list are expert of distance matrices and can answer your > > question. > > Have a nice week, > > Ákos > > > > 2019.06.03. 17:44 keltezéssel, Gian Maria Niccolò Benucci írta: > &g

Re: [R-sig-eco] reorder vegdist objects

ecalculate > the distance matrix (e.g. due to computer capacity or time), you can > reorder the distance matrix (both the rows and columns). > dist_b_reordered2 <- as.dist(as.matrix(dist_b)[attr(dist_a, "Labels"), > attr(dist_a, "Labels")]) > all.equal(dist_

[R-sig-eco] reorder vegdist objects

Hello, I have two vegan::vegdist objects I want to use into a vegan::mantel test. However, rows and columns of the two objects are not in the same order. Is there a way to reorder them one another? For example, >dist_a Lycovolu Hupeaust Lycofast Lycodeut Hupeaust 0.9045557 Lycofast

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

) main > effects and all these terms are marginal and can be removed, whereas the > latter Stage*Growhouse expands to explicit main effects and interaction > effects, and only the interaction effects are marginal and can be removed. > This is also reflected in the degrees of freedom in

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

nly the interaction effects are marginal and can be removed. > This is also reflected in the degrees of freedom in your anova table: In > the first case Stage:Growhouse has 3 df, and in the latter only 1 df (and > the main effects ignored had 2 df). > > Ciao, Giari > > > On 29 O

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

Hello Jari, It is a little bit confusing. If A*B unfolds in A+B+A:B then A:B is the real interaction component. So, which if the code below will test the variance for the interaction alone? > adonis2(t(otu_fungi_out) ~ *Stage : Growhouse*, data=metadata_fungi_out, by = "margin",

[R-sig-eco] How important is to have a balanced design for adonis?

Hello dear ecologists, I have a question for you in here. How important is to have a balanced design for adonis? In other words, how sensitive is adonis() to differences in sample numbers within the groups I am comparing? To link this question to the reality, I am trying to compare the microbial

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

Hello all, thank you for the interesting discussion on the topic. I have an additional question that i thought would worth to ask directly here instead of opening a new thread for it. How sensitive is adonis() to differences in sample numbers of the groups I am comparing? To be more precise, I am

[R-sig-eco] procrustes() and protest() in vegan: any hints on the interpretation?

Good morning r-sig-ecologists, I have a question for you on how to have a correct interpretation of protest() output. I have read the R documentation where it is reported that a correlation-like statistics is computed from the symmetric Procrustes sum of squares also called squared m12 =

Re: [R-sig-eco] Complete lecture Multivariate Statistics freely available

That's really good and useful, thank you for sharing! G. On 27 January 2017 at 06:11, Tania Bird wrote: > Yes really an amazing resource!! > > Thank you so much for making it available. > > Tania > > > On 27 Jan 2017 12:35, "Ralf Schäfer" wrote:

[R-sig-eco] How to calculate relative abundance along taxonomical hierarchy

Hello everyone, I am working on a fungal dataset with 151 OTUs distributed in 20 samples. I have imported it as phyloseq object and as normal species matrix as well to work with the vegan package. I am trying to find a way to get relative abundances at different hierarchical level goruping the

Re: [R-sig-eco] How to calculate relative abundance along taxonomical hierarchy

) function in the mefa4 package to get your relative abundances. Cheers, Peter Gian Maria Niccolò Benucci gian.benu...@gmail.com ezt írta (2015. június 25., csütörtök): Hello everyone, I am working on a fungal dataset with 151 OTUs distributed in 20 samples. I have imported it as phyloseq object

Re: [R-sig-eco] How to calculate relative abundance along taxonomical hierarchy

need to transpose or adjust the code I suggested before. Peter Gian Maria Niccolò Benucci gian.benu...@gmail.com ezt írta (2015. június 25., csütörtök): Hello, thank you for the replies. My dataset is something like this: datafungi BR1 BR2 BR3 BR4 BR5 F1 F2 F3 F4

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

For SIMPER you can read this thread: https://www.researchgate.net/post/What_do_you_think_about_Similarity_Percentage_analysis_SIMPER_to_measure_species_indicator_value Moreover read the function help(simper) carefully, because: The results of 'simper' can be very difficult to interpret. The

Re: [R-sig-eco] [Fwd: Re: how to detect different species among samples]

Dear Martin and Mario, thanks a lot, both of your code work greatly... Now I have species that are common between two selected sites, but how to to detect species that are unique between two selected sites? in other words which species is present in the site A and which other in the site B?

Re: [R-sig-eco] [Fwd: Re: how to detect different species among samples]

Dear Martin and dear all, I tried your approach but I suppose it does not work... my commands are the following, where's my mistake? head(dune) Belper Empnig Junbuf Junart Airpra Elepal Rumace Viclat Brarut Ranfla Cirarv 2 3 0 0 0 0 0 0 0 0 0

Re: [R-sig-eco] how to detect different species among samples

Hi Martin, thanks a lot. Also your commands are working... It's very nice to see how different solutions in R can be found for a single problem. I just have another question now, but... if I would know which species are in common (and which not) between two particular selected samples? Thanks for

[R-sig-eco] how to detect different species among samples

Hi all R-sig-ecologists, Sorry for the very simple and probably stupid question. I was wandering if exist a simple method or a function in R, to detect which different species are present among the samples of a given data community matrix. Thanks a lot in advance, -- Gian

Re: [R-sig-eco] how to detect different species among samples

wrote: Hi Gian, I don't understand what you're trying to do. Can you give a simple example of your data and what your results should be? Sarah On Saturday, February 1, 2014, Gian Maria Niccolò Benucci gian.benu...@gmail.com wrote: Hi all R-sig-ecologists, Sorry for the very simple

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

Hi, Thank you very much for your help! G. On 19 July 2012 18:13, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Mon, 2012-06-25 at 16:46 +0200, Kay Cichini wrote: Hi! library(vegan) data(dune) sol - metaMDS(dune) # use argument air! see ?orditorp: plot(sol, type = n)

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

Hi community, Very simple question. How to avoid overlap plot of species in a metaMDS() diagram? I used this command... text(metaMDS_new2, display=c(species), cex=0.6) but some species are plotted one over the other and is not simple to read the diagram. Thanks for helping, -- Gian

[R-sig-eco] pooled versus averaged samples in diversityresult function

Hallo ecologists, I know that this is not the right place where to post my help-request so I say sorry in advance. My question concern results of biodiversity indices with diversityresult() tha I used to describe the diversity of two different, comparable fungal communities. This is what I got:

Re: [R-sig-eco] diversityresult function - BiodiversityR package

Dear Roman, I have that book. But it is no mention on how the funtion calculate diversity for different methods. I assume someone used that function before, do anyone? Thanks a lot! Cheers, -- Gian 2012/3/30 Roman Luštrik roman.lust...@gmail.com If you know BiodiversityR, you probably

Re: [R-sig-eco] diversityresult function - BiodiversityR package

From: r-sig-ecology-boun...@r-project.org [ r-sig-ecology-boun...@r-project.org] on behalf of Gian Maria Niccolò Benucci [gian.benu...@gmail.com] Sent: 30 March 2012 11:57 To: r-sig-ecology@r-project.org Subject: [R-sig-eco] diversityresult function - BiodiversityR package Hi all

[R-sig-eco] SIMPER analysis

: https://github.com/jarioksa/**vegan/issues/3https://github.com/jarioksa/vegan/issues/3 Let me know if your facing any problems with this function. Cheers, Edi On 09/03/12 09:51, Gian Maria Niccolò Benucci wrote: Hi members, Do anyone know if SIMPER analysis (Clarke 1993) is implemented

[R-sig-eco] stressplot() in vegan metaMDS

Hi everyone, I am doing a metaMDS in a sqrt() dataset of 24 samples. The NMDS diagram is ok but when I try to see the Shepard diagram I have this result: stressplot(metaMDS3) Using step-across dissimilarities: Too long or NA distances: 147 out of 276 (53.3%) Stepping across 276

Re: [R-sig-eco] taxonomic diversity and distinctness - taxondive() in vegan package

2012/2/23 Jari Oksanen jari.oksa...@oulu.fi On 21/02/2012, at 13:38 PM, Gian Maria Niccolò Benucci wrote: Dear All, I just want to ask if someone can explane me how the steps are calculated in taxa2dist(). I would know how steps are calculated because it is foundamental to define

Re: [R-sig-eco] taxonomic diversity and distinctness - taxondive() in vegan package

OTU30 OTU31 OTU32 UE1 UE2 UE3 UE4 [37] UE5 UE6 2012/2/16 Jari Oksanen jari.oksa...@oulu.fi On 16/02/2012, at 18:39 PM, Gian Maria Niccolò Benucci wrote: Hi everybody, I am here for asking some kind of help about taxonimic diversity and distinctness indices, from taxondive

Re: [R-sig-eco] non-metric MDS comparison - vegan vs. ecodist packages

...@ucl.ac.uk On Mon, 2012-02-20 at 16:28 +0100, Gian Maria Niccolò Benucci wrote: Hi r-sig-ecology Members, I would please you to examine the differences I found in metaMDS() and nmds() outputs and possibly draw some conclusions. As I wrote in past emails I have 24 samples of ectomycorrhizal

Re: [R-sig-eco] non-metric MDS comparison - vegan vs. ecodist packages

gavin.simp...@ucl.ac.uk On Mon, 2012-02-20 at 17:24 +0100, Gian Maria Niccolò Benucci wrote: Dear Gavin, Thank you very much. I tried with your advice but the result is almost unchanged... Any further advice?? Yeah, what Sarah said. Read the documentation; the two functions use different

[R-sig-eco] taxonomic diversity and distinctness - taxondive() in vegan package

only 15 points, instead of 24 that is the overall sample number, becasue there is an overplotting...do is it possible? Moreover, there is the possibility to plot in the funnel diagram the name of the samples? Thank you to everyone, G. -- Gian Maria Niccolò Benucci, Ph.D. Department of Applied

Re: [R-sig-eco] question concerning nmds.min

2012/2/2 Gian Maria Niccolò Benucci gian.benu...@gmail.com: ... Which among the 50 configuration the functions chose? How to look to its stress and R2 values? Forgot about the R-squared - according to the vegan FAQ 1 - stress^2 transforms nonlinear stress into quantity analogous to squared

Re: [R-sig-eco] question concerning nmds.min

() is that it lets you choose a particular dimension solution rather than the lowest available. For your example, the same thing can be achieved with iris.nmds$conf[[which.min(iris.nmds$stress)]] Sarah 2012/2/2 Gian Maria Niccolò Benucci gian.benu...@gmail.com: Hi all, I am trying to run a nmds

Re: [R-sig-eco] question concerning nmds.min

of discussion and brainstorming, just let me know how and if I can. I am a fungal eco-biologist (if the term is correct). Cheers, G. -- Gian Maria Niccolò Benucci, Ph.D. Department of Applied Biology University of Perugia Borgo XX Giugno, 74 06121 - Perugia, ITALY Tel: +390755856433 Email: gian.benu

Re: [R-sig-eco] metaMDS result

very much, G. 2012/2/2 Jari Oksanen jari.oksa...@oulu.fi On 02/02/2012, at 19:43 PM, Gian Maria Niccolò Benucci wrote: Hi Members, I tried to use a metaMDS to explore my two fungal communities data. That's the result: Call: metaMDS(comm = species.data_log, distance = bray, k

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

be tested. G gabriel On 11/16/11 11:02 PM, Gavin Simpson wrote: On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccolò Benucci wrote: Hi all, I had 84 samples collected in 7 different sites. In each sample were individuated the different fungal species and recorded. I would test

[R-sig-eco] interpreting adonis results

-11-16 at 03:43 +0100, Gian Maria Niccolò Benucci wrote: Hi all, I had 84 samples collected in 7 different sites. In each sample were individuated the different fungal species and recorded. I would test if exist a real difference between the sites and if exist a sort of site effect

[R-sig-eco] interpreting adonis results

Hi all, I had 84 samples collected in 7 different sites. In each sample were individuated the different fungal species and recorded. I would test if exist a real difference between the sites and if exist a sort of site effect that structure the fungal communities... Then, I did adonis test

Re: [R-sig-eco] Species richness in R

Dear Manuel, I did it with vegan function *diversityresult().* Look to R help for this function there are many parameters you can modify and add to it. The code is: library(vegan) diversityresult(X, index=richness) I hope it helps, Gian -- Gian Maria Niccolò Benucci Ph.D. Candidate

[R-sig-eco] characters size in plotting dendrograms with diana funcion

Hi everybody, I have plotted a diana dendrogram. The names of samples under the dendrogram lines are unfortunately too big. How do I reduce samples name down into the dendrogram plot? Every advice is greatly welcome, thank you in advance! -- Gian [[alternative HTML version deleted]]

Re: [R-sig-eco] Understanding NMS (non-metric multidimensional scaling) outputs

Thank you a lot for your aid... Cheers, Gian On 14 December 2010 13:21, Wade Wall wade.w...@gmail.com wrote: Gian, I have found Analysis of Ecological Communities by McCune and Grace to be a really good resource for understanding NMDS and other multivariate techniques. It has

[R-sig-eco] Understanding NMS (non-metric multidimensional scaling) outputs

Hi everybody, I was wondering if exist something where to read about NMS outputs. In particular about commenting a generated NMS ordination graph. Thank you very very much in advance, Gian [[alternative HTML version deleted]] ___

Re: [R-sig-eco] ANOSIM test

, for a univariate ANOVA test. When including the results in a paper or dissertation, it would be normal to quote both values (R and significance). I hope that's helpful, Barbara - Original Message - From: Gian Maria Niccolò Benucci gian.benu...@gmail.com Date: Tuesday, June 8, 2010 4:57 am

[R-sig-eco] How calculate Sørensen and Bray-Curt is coefficients? vegan package

software, is it true? Because I try to find the correct function fot that but I didn't find it already. Thanks a lot in advance to Jari who surely concern with my question, and to all will help me in that. G. -- Gian Maria Niccolò Benucci Ph.D. Candidate Department of Applied Biology - University

Re: [R-sig-eco] ANOSIM test

0034 956832612 ext. 316 ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Gian Maria Niccolò Benucci escribió: Barbara, Thank you very much, indeed I red the two values on a paper, that were of R=0.15 and P=0.006, and they states that the difference between the two groups

Re: [R-sig-eco] How calculate Sørensen and Bray-Curt is coefficients? vegan package

Hi, Thanks a lot, I've found the functions: vegdist and designdist. Cheers, G. On Wed, Jun 9, 2010 at 11:26 AM, romunov romu...@gmail.com wrote: ?vegdist On Wed, Jun 9, 2010 at 11:21 AM, Gian Maria Niccolò Benucci gian.benu...@gmail.com wrote: Hi all again, I have red

[R-sig-eco] Fwd: ANOSIM test

to propose to people just starting with statistics and I still use it when I need a quick overview on my analyses): http://folk.uio.no/ohammer/past/ Cheers Angélique Gian Maria Niccolò Benucci wrote: Hi Angélique, Many many thanks about your help, I will read the paper carefully. It's always

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

-- Forwarded message -- From: Gian Maria Niccolò Benucci gian.benu...@gmail.com Date: 2010/5/22 Subject: Re: [R-sig-eco] Graphical parameters in metaMDS To: Jari Oksanen jari.oksa...@oulu.fi Jari, Sorry, in the future I will spcify the pakages where the functions

[R-sig-eco] Graphical parameters in metaMDS

will be surely appreciated, many thank you in advance... Gian -- Gian Maria Niccolò Benucci Ph.D. Candidate Department of Applied Biology - University of Perugia Borgo XX Giugno, 74 I-06121 - Perugia, ITALY Tel: +39.0755856433 Fax: +39.0755856069 Email: gian.benu...@gmail.com [[alternative HTML

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

*random* effects in adonis(), which was intended as the main message of my previous posting on this issue. They are all fixed effects. Cheers, Jari Oksanen -- Dr. Gian Maria Niccolò Benucci Department of Applied Biology - University of Perugia Borgo XX Giugno, 74 I-06121 - Perugia, ITALY

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

on that... Cheers, Gian -- Dr. Gian Maria Niccolò Benucci Department of Applied Biology - University of Perugia Borgo XX Giugno, 74 I-06121 - Perugia, ITALY Email: gian.benu...@gmail.com Tel: +39.075.5856433 2009/12/10 Maria Dulce Subida mdsub...@icman.csic.es Dear Gian, I'm still not quite sure

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

%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- Dr. Gian Maria Niccolò Benucci Department of Applied Biology - University of Perugia Borgo XX Giugno, 74 I-06121 - Perugia, ITALY Email: gian.benu...@gmail.com Tel: +39.075.5856433 [[alternative HTML version deleted

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

Hi all again, And thank you all for the kind responses... I do not want to torture myself for sure... :) I red (lot of) publications about fungal community ecology studies (soil fungi), my research field indeed, and all uses NMDS or DCA as ordination techniques... So, I am only trying to do my

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

Jari, I am here again ... :) So, to try having a comparison of the real goodness of my metaMDS data I tried to perform a DCA (with same input table) Then please forgive me if I do somethign wrong with it... That's my R code: decorana(sqrtABCD, iweigh=0, ira=0) - DCA.1 DCA.1 Call: decorana(veg

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

I am here again ... :) So, to try having a comparison of the real goodness of my metaMDS data I tried to perform a DCA (with same input table) Then please forgive me if I do somethign wrong with it... That's my R code: decorana(sqrtABCD, iweigh=0, ira=0) - DCA.1 DCA.1 Call: decorana(veg =

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

Okey, I understood... I have a matrix of 40 rows (samples) and 29 columns (species). In the ordination graph the data divide in two clades ( as i supposed they must to)... and that's my best solution for reduce the Stress... metaMDS(sqrtABCD, distance = bray, k = 23, trymax = 50, autotransform

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

Jari, Yes, you right, I am sorry I didn't say that I was talking about Euclidean measure of distance in that passage, I know that other distance are different, and finally I understood the non-linear regression stuff, now is much more clear! If you have some good book titles I would appreciate a

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

Hi Hi there, I am trying to use funcion metaMDS (vegan pakage) for Community Ecology data, but I find no way to calculate the expressed variance of the first 2 axis? is there a way to do that? Thanks a lot in advance, Gian [[alternative HTML version deleted]]