Re: [R-sig-eco] Adonis output with or without strata

Dear list members, Thanks Jakob Russel for your last email. This discussion is really useful to me in conducting the right analyses on my data. I�m hoping you won�t mind pursuing it. I ran adonis again: ad4 <- adonis(dist ~ Island + Dis + Island:Dis, data = meta)

Re: [R-sig-eco] Adonis output with or without strata

Hi Jakob, Thank you for your time and useful answers. I had tried to include Island as a fixed factor earlier and had a significant result for both factors. I got confused on how to interpret this output. I was interested in the difference between Healthy and Diseased but Island had an

Re: [R-sig-eco] Adonis output with or without strata

Dear Gaëlle, The p-values in PERMANOVA are generated by permutations. These permutations are by default free, but they can be constrained by the strata factor. The strata argument only affects the permutations, and hence will only affect the p-value. The Sum of Squares (and R2) are only based on

[R-sig-eco] Adonis output with or without strata

Dear list members, I am having trouble understanding the output of an adonis model I am running first with then without the argument �strata� in the formula. I have seen this question asked before but no answer were provided. I would like to compare microbial communities associated with

Re: [R-sig-eco] Adonis for significance of clusteredness from hclust (vegan package)

pvclust is a good package to create and test significance of cluster groups. 2016-10-05 11:31 GMT-03:00 Pierre THIRIET : > Dear Ansley, > > I agree with Zoltan. > > I suggest SIMPROF test in package "clustsig". A complimentary package > for use with hclust; simprof

Re: [R-sig-eco] Adonis for significance of clusteredness from, hclust (vegan package)

.org wrote: > Re: [R-sig-eco] Adonis for significance of clusteredness from > hclust (vegan package) 2016.10.03. 21:52 keltez?el, Ansley Silva ?a: > Hello: > > I have created a dendrograms using hierarchical cluster analysis with the > vegan package (function: hclust

Re: [R-sig-eco] Adonis for significance of clusteredness from hclust (vegan package)

Dear Ansley, I agree with Zoltan. I suggest SIMPROF test in package "clustsig". A complimentary package for use with hclust; simprof tests to see which (if any) clusters are statistically different. The null hypothesis is that there is no a priori group structure. See Clarke, K.R.,

Re: [R-sig-eco] Adonis for significance of clusteredness from hclust (vegan package)

Dear Ansley, I cannot answer your question, I hope someone else will answer. I'd rather point out a problem in your approach. Statistical tests were developed for testing difference between a priori groups, thus estimated Type I error rate is valid only for this situation. When you calculates

[R-sig-eco] adonis or other multi-variate approaches to examine community change over time given main effect of treatment

Hello All, I have a large data set where I am interested in answering the question of whether initial conditions (i.e. our initial treatments) influenced the community composition over time. We have 10 replicates for each treatment and species abundances for 15+ species. My question is, I have

[R-sig-eco] adonis with blocking (not nesting)

Dear R for ecology experts, I have found many discussions online about blocking and nesting in adonis, but no answers for blocking. I have community data with abundances within 42 aquatic genera (final.fd[,9:36]) from 2 types of streams (type). Stream samples were paired (pair) as a blocking

[R-sig-eco] Adonis model help

Hi all, I'm new to community data analysis in R and was hoping to get some feedback on my intended approach using adonis. The primary aim is to test the effect of treatment group (FOOD: F or N) on community assemblage. I have repeated measures data so I have included SITE ID as a random factor

[R-sig-eco] adonis() and collinearity

Dear all, if I use only continuous explanatory variables in the adonis() function it is like a multiple linear regression with dissimilarities. In multiple regression with highly correlated exp. variables I have the problem with multicollinearity and an increasing standard error of the

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

Dear Jonas Kuppler, On 17/09/2014, at 16:06 PM, Jonas Kuppler wrote: if I use only continuous explanatory variables in the adonis() function it is like a multiple linear regression with dissimilarities. In multiple regression with highly correlated exp. variables I have the problem

[R-sig-eco] Adonis Vs. AMOVA

I am currently trying to figure out the differences between Adonis {vegan} and Analysis of Molecular Variances AMOVA {e.g. Ade4}. I know that Adonis tests if the position of the centroids (belonging to groups or species) are different and that this is an approximation of compositional (beta

Re: [R-sig-eco] adonis

Alan, A few comments on your procedure. You have two non-standard things in your message: you try to do something that looks like post hoc tests, and you use non-standard contrasts. There is nothing post hoc in your post hoc tests. What you do is that you break your factor variable into

[R-sig-eco] adonis

Hi all, Im using adonis for some plant community analysis and have been following theBioBucket example of how to posthoc tests ( http://thebiobucket.blogspot.ch/2011/08/two-way-permanova-adonis-with-custom.html ) data(dune) data(dune.env) ad1 - adonis(dune ~ Management, data=dune.env,

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

, March 09, 2013 9:09 PM To: JOHN S BREWER Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Adonis and Random Effects Hi Steve and R list, I was hoping you could clarify something you mentioned in previous post. A quick recap... I have a split-plot design where I determined

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

Steve From: Erin Nuccio [enuc...@gmail.com] Sent: Saturday, March 09, 2013 9:09 PM To: JOHN S BREWER Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Adonis and Random Effects Hi Steve and R list, I was hoping you could clarify something you mentioned

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

and others about the versions of BiodiversityR and R used. Hope this helps Steve From: Erin Nuccio [enuc...@gmail.com] Sent: Saturday, March 09, 2013 9:09 PM To: JOHN S BREWER Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Adonis

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

PM To: JOHN S BREWER Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Adonis and Random Effects Hi Steve and R list, I was hoping you could clarify something you mentioned in previous post. A quick recap... I have a split-plot design where I determined the microbial

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

Hi Steve and R list, I was hoping you could clarify something you mentioned in previous post. A quick recap... I have a split-plot design where I determined the microbial communities at 3 grasslands (see post script for design). I am trying quantify the how much of my community can be

[R-sig-eco] adonis and temporal changes

Dear all, I would like to test changes in species dissimilarity matrices over time, taking into account that the measurement are repeated in each site over years. I used the adonis function: adonis(diss.matrix~year, strata=site). However if I do the same model entering site as an additional

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

Dear Valérie, If I remember well, your design includes: Isolation categories: 3 levels Sites: nested within Isolation categories (10 levels, a total of 30 sites) How many replicates per site and time? Time:? how many years you have? Only one sampling per year? Within sites and years, samples

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

On 18/02/2013, at 14:04 PM, Pierre THIRIET wrote: Dear Valérie, If I remember well, your design includes: Isolation categories: 3 levels Sites: nested within Isolation categories (10 levels, a total of 30 sites) How many replicates per site and time? Time:? how many years you have? Only

[R-sig-eco] adonis and temporal changes

Thank you for these explanations. If I put strata=site, this means that for each site my dissimilarity matrix of year 1 and year 2 will be permuted and the observed changes compared to these random permutation? Adding site as a fixed factor then ensure that I am testing changes in time site by

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

Valerie, Adonis does not define fixed or random effects, and you therefore cannot define multiple error terms. However, if your model statement looks something like this - isolation*year + site, strata = site - then you will get the correct test for the isolation x year interaction and the

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

an environemental gradient (continuous, one value pro site, constant over the years). Is it possible to include it? Best wishes Valerie Message du 18/02/13 à 15h41 De : Steve Brewer A : v_coudr...@voila.fr, r-sig-ecology@r-project.org Copie à : Objet : Re: [R-sig-eco] adonis and temporal changes

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

an additional question: I have also an environemental gradient (continuous, one value pro site, constant over the years). Is it possible to include it? Best wishes Valerie Message du 18/02/13 à 15h41 De : Steve Brewer A : v_coudr...@voila.fr, r-sig-ecology@r-project.org Copie à : Objet : Re: [R-sig

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

-project.org Copie à : Objet : Re: [R-sig-eco] adonis and temporal changes Valerie, If I understand your design correctly, you're doing a repeated measures analysis, in which isolation is a between-subjects (I.e., between-sites) effect. Year and the year x isolation interaction are within-subjects

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

Thanks Steve and Jari for your responses. I really do appreciate it -- trying to analyze this data has been a challenge! Based on both your responses, it seems like I won't be able to get adonis to do the appropriate tests for the Grassland effect (since I do not know how to design custom

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

On 04/02/2013, at 09:14 AM, Erin Nuccio wrote: Is adonis capable of modeling random effects? No, adonis does not know random effects. The significance tests in adonis() are based on permutations. The key question for random effects is: can you design a permutation matrix that treats some

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

Erin, There have been a lot of similar queries (e.g., repeated measures, nested permanova). Jari can correct me if I am wrong, but as far as I know, no one has developed a way to define multiple error terms in adonis. You can use adonis, however, to get the split-plot effects. If you want to

[R-sig-eco] adonis and negative F-values

Dear all, I used adonis to perform a test of the pairwise site dissimilarity indices proposed by Baselga (2010, 2012) in the package betapart. I am concerned about my results because I get some negative F-values. I read in another post that this may happen because of the presence of negative

[R-sig-eco] Adonis and Random Effects

Hello List, Is adonis capable of modeling random effects? I'm analyzing the impact of a treatment on the microbial community in a split-plot design (2 treatments per plot, 4 plots per grassland, 3 grasslands total). I would like to quantify how much of the variance is due to the Treatment

Re: [R-sig-eco] adonis: error in rowSums

On Wed, Feb 8, 2012 at 4:10 PM, Caroline Wallis c.wal...@worc.ac.uk wrote: I am trying to use the 'adonis' function in the 'vegan' package to assess differences in water depth and water velocity between areas of a river channel categorised by surface flow type (6 types in total, unequal

Re: [R-sig-eco] adonis: error in rowSums

Dear Caroline, It seems that you response (community-like) data are Depth and Velocity. Than a dataframe with these two variables should be on the left hand side of the formula, while SFT on the right hand side. Something like adonis(LB[,2:3] ~ SFT, data=LB, method=canberra) should work. Cheers,

[R-sig-eco] adonis: error in rowSums

I am trying to use the 'adonis' function in the 'vegan' package to assess differences in water depth and water velocity between areas of a river channel categorised by surface flow type (6 types in total, unequal sample sizes). Sample Data (LB): SFT Depth Vel BSW 0.181.2 BSW

Re: [R-sig-eco] adonis: error in rowSums

On Wed, Feb 8, 2012 at 4:10 PM, Caroline Wallis c.wal...@worc.ac.uk wrote: I am trying to use the 'adonis' function in the 'vegan' package to assess differences in water depth and water velocity between areas of a river channel categorised by surface flow type (6 types in total, unequal

[R-sig-eco] adonis and betadisper interpretation

Hi, I have some trouble with interpretation of R functions: adonis and betadisper. I am interesting in understanding if the communities differ according to land use treatment (3 treatments) and time (6,12,18,24 and 30 months). I know that adonis works on the centroids for the groupings and

Re: [R-sig-eco] adonis question

Cichini Sent: Friday, 24 June 2011 9:31 PM To: r-sig-ecology Subject: [R-sig-eco] adonis question hi all, i played around with adonis and came across a result that i can't explain - more precisely i get a sign interaction-effect where i suppose there should be none: library(vegan) # species

Re: [R-sig-eco] adonis question

: Friday, 24 June 2011 9:31 PM To: r-sig-ecology Subject: [R-sig-eco] adonis question hi all, i played around with adonis and came across a result that i can't explain - more precisely i get a sign interaction-effect where i suppose there should be none: library(vegan) # species matrix/df

[R-sig-eco] adonis and contrasts

hello all, in https://stat.ethz.ch/pipermail/r-sig-ecology/2010-April/001221.html jari oksanen describes how to use custom contrasts with adonis. i'm curious whether there's also a way to yield the according significance tests - else i don't see much purpose in customizing your

[R-sig-eco] adonis once again

Dear list members, I have a question again on adonis and whether the interpretation is correct. I must admit that I am a big fan of ANOSIM, I think it is pretty simple to explain, in contrast to adonis. I have plant species dataset based on a literature review. I have calculated the

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

Hi Jari, Thanks for your prompt reply. That clears things up, although you've left me with a doubt. You said: Indeed, adonis() can use only continuous variables, it is documented to do so, and this was initially intended. Are you saying that categorical variables should not be used in

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

On 10/03/11 11:25 AM, alfredo Tello alfredote...@gmail.com wrote: Hi Jari, Thanks for your prompt reply. That clears things up, although you've left me with a doubt. You said: Indeed, adonis() can use only continuous variables, it is documented to do so, and this was initially intended.

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

Thanks Jari! Sorry if I wasn't clear enough at first. All the best, A -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/adonis-with-continuous-variables-tp6155914p6157213.html Sent from the r-sig-ecology mailing list archive at Nabble.com.

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

Hi Jari (and everyone else who might read this), Just one last thing (I hope I'm not being annoying! ). I believe this can be of interest to other people as well. In a recent paper in the ISME (International Society for Microbial Ecology) Journal, Thomas Bell used adonis to test for evidence of

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

On Thu, 2011-03-10 at 01:25 -0800, alfredo Tello wrote: Hi Jari, Thanks for your prompt reply. That clears things up, although you've left me with a doubt. You said: Indeed, adonis() can use only continuous variables, it is documented to do so, and this was initially intended. I

[R-sig-eco] adonis with continuous variables

Hi Folks, The adonis documentation in vegan says that adonis accepts categorical factors and/or continuous variables. I was aware (have seen it posted somewhere else) that adonis could be run using a continuous variable as a co-variate, but not that it could (or was initially intended to) be used

[R-sig-eco] adonis to test difference in sums of squares partitioning across treatments?

Dear list, We are working with a dataset of bird community composition across four regions, each of which contain three land use treatments. We are interesting in understanding if the community dissimilarity within regions and between regions differs according to land use treatment. I

Re: [R-sig-eco] adonis to test difference in sums of squares partitioning across treatments?

-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Andy Rominger Sent: Friday, 17 December 2010 5:17 AM To: r-sig-ecology@r-project.org Subject: [R-sig-eco] adonis to test difference in sums of squares partitioning across treatments? Dear list, We are working

Re: [R-sig-eco] adonis to test difference in sums of squares partitioning across treatments?

= site.data) Hope that helps, Etienne -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Andy Rominger Sent: Friday, 17 December 2010 5:17 AM To: r-sig-ecology@r-project.org Subject: [R-sig-eco] adonis to test difference

[R-sig-eco] ADONIS and pseudoreplications

Dear listers, I intended to send a separate question but it fell under comments on Eduard Szöcs's question. Sorry for that. The problem: I collected aquatic insect larvae from 17 sites three times (spring, summer, autumn), giving a total of 51 samples. During each sampling campaign several

[R-sig-eco] adonis and model selection

Dear list, I was wondering if there is a possibility to do model selection with the method adonis of the package Vegan. If so, could any one explain me about it or give me a hint were to look? Kind regards, Maarten ___ R-sig-ecology mailing list

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

On 5/08/10 09:51 AM, Maarten de Groot maarten.degr...@nib.si wrote: Dear list, I was wondering if there is a possibility to do model selection with the method adonis of the package Vegan. If so, could any one explain me about it or give me a hint were to look? Maarten, Not automatically:

[R-sig-eco] adonis and distance metrics

Dear R-sig users, In a full-factorial mesocosm experiment (80 mesocosms: three factors with two levels each and hence 10 replicates per treatment combination) we measured the aboveground biomass of 28 plant species that were sown in this experiment. Results are given as abundances (kg/m²)

Re: [R-sig-eco] adonis and distance metrics

Hi Wout, This is always tricky. There are so many different metrics out there that it can be really confusing to choose the right one. Legendre and Legendre 1998 Numerical Ecology go at great length at describing many of them so that's a good place to start. The danger is that, not having any

[R-sig-eco] adonis and contrasts

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 use contrasts instead (treatments 1 v 2 + 3, and 2 v 3). Oksanen (2009) mentions

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] adonis and contrasts

Dear Jari, Thank you very much for your help. I have tried both methods, but neither of which seem to have worked. This is most likely an oversight on my part so I have included an example of the alternative method provided with the hope that I am simply missing something. dataset[1:5,] ID

[R-sig-eco] adonis question

Hi After performing a permutational ANOVA with adonis in vegan, is there a way to do multiple comparisons for significant factors with more than 2 levels as well for significant interactions? Any help would be very much appreciated Thanks, Jaime [[alternative HTML version

Re: [R-sig-eco] adonis question

Hi Jaime, The interactions are just a matter of defining the formula as such, e.g. adonis(dist~factor1*factor2). I suppose, a multiple comparison (with the reasoning of a post-hoc test) can just be done using adonis() for pairwise comparisons and then use p.adjust(). Cheers, gabriel On

[R-sig-eco] adonis model specification

Dear R helpers, I have collected species composition data (counts of 24 species)from 16 plots. I am interested in seeing how different the plots are from each other and how this changes over time. My design is as follows: I repeatedly sampled the plots each month for 11 months. The plots are

Re: [R-sig-eco] adonis model specification

Christine, There is no summary method for adonis. After calling the function, simply use print: x - adonis(...) x And you are right, you can supply raw data and use the method argument in adonis to define dissimilarity index (which is bray by default). Cheers, Peter Péter Sólymos Alberta

[R-sig-eco] Adonis vs anosim/mrpp in vegan

I am curious about the suggestion and warnings about using adonis instead of the functions anosim and mrpp in the vegan package. Is this suggestion based on the fact that MANOVA using distance matrices is more robust and powerful than anosim and mrpp statistically speaking and should be used

Re: [R-sig-eco] adonis/vegan

On Wed, 2008-07-02 at 10:37 +0100, Diego Fontaneto wrote: Why does order matter in specifying a model in adonis? Because they are sequential sums of squares. See the Value section of ?adonis. snip / Another question