Questions tagged [vegan]

R package for community and vegetation ecology. Includes ordination methods, diversity analysis, etc.

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Environmental Vector Fit to NMDS Data

I am new to doing NMDS in R, and I have a question about how the vectors that characterize the fit of environmental data. I am exploring how the concentrations of metals in sediment affect benthic ...
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Should I pool samples or leave them separate before running a PERMANOVA?

I have a dataset of fish species from different sites within a harbour collected over 17 years. The dataset consists of 1,042 sampling transects collected at 6 specific locations where fish were ...
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NMDS with species-sites matrix and iterations

How could I conduct an NMDS-ordination for a species-sites matrix with multiple iterations? I know how to conduct a NMDS with a "normal" species-sites matrix, but I couldn't find any ...
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104 views

How to properly perform constrained ordination (RDA) when the sums of the rows of the constraining matrix are equal to the same value?

When performing an RDA where the constraining matrix displays equal sums of rows, the last column in the matrix is always considered aliased and therefore dropped. I am asking why this happens and how ...
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R: vegan/permute: additional level of nesting for pseudoreplicates in a split plot

I am trying to investigate how to set up a permutation scheme for community data originating from a split plot experiment with pseudoreplicates at the lowest level. A theoretical design could be the ...
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R: When to set bias.adjust = TRUE in vegan::betadisper?

I am trying to test if my data have homogeneous variance using vegan::betadisper() in R. I read the help for the function but it only says that is appropriate when ...
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9 views

Does the order of terms matter in adonis.II?

I'm a bit confused. The order of terms matter in adonis2, but how about adonis.II? Somebody wrote here : https://stat.ethz.ch/pipermail/r-sig-ecology/2018-October/005822.html that ordering, does not ...
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47 views

Is it possible to use a PERMANOVA (adonis / R) on a time series - are there any alternatives?

I'm having trouble with fitting a PERMANOVA (adonis) to my data and am actually not sure if it is possible at all. I have a pitfall arthropod data set for 5 research areas and 3 consecutive field ...
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107 views

How does PERMANOVA use degrees of freedom in comparison to a linear model (R software)?

I am a long time user of the forum but first time poster. My question is unrelated to a specific dataset but on the internal workings of a PERMANOVA in R (adonis2 ...
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45 views

Accounting for spatial structure in constrained ordination analysis (vegan)

I am looking to use ordination to test whether certain environmental measures influence the microbial community in soil samples. I am a bit confused about the correct way to define the model and ...
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105 views

How to evaluate permutation tests in vegan when strata are are not balanced

I have a multivariate data set of 12 sites, and 4 plots per site, except one site which only has three plots. There two variables of interest: site_type, which is ...
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45 views

vegan::adonis2() for randomized complete block design with main-plot, split-plot, and nested effects

I coded my adonis2 formula following the answer below. The original r-forge is not accessible anymore, though. I used the suggested model on my data but I got the ...
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14 views

Interpretation of eigenvalues from `decorana()` summary table

I just want to make sure I understand the example in the vegan package. Per the summary table on page 2 of this document, can I say that the first two axes of the ...
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135 views

How does adonis2 (Permanova) handle continuous variables?

I'm working with a matrix of community count data. We collected both continuous and categorical environmental information.I would like to use adonis2 (R package vegan) to apply permutational analysis ...
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1answer
119 views

Environmental variable vector in NMDS

I am using Non-metric MultiDimensional Scaling (NMDS) on a Bray-Curtis dissimilarity matrix. Then, I am trying to link the resulting NMDS axes (let's say "components") to environmental ...
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20 views

calling scores “changing” NMDS values from envfit() and R2 and P values

I have been following the excellent guide: NMDS ordination in R I wish to use the envfit function to see which of my environmental parameters correlate with community data dissimilarity. When I run ...
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856 views

How is pairwise PERMANOVA/adonis a valid non-parametric approach for pairwise comparisons

Assume that we have taken independent random samples of several individuals from 5 locations that represent 5 populations. The design is fairly unbalanced: the number of individuals sampled from each ...
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28 views

Should you standardize and exclude correlated environmental variables prior to fitting them onto an ordination using envfit()?

I plan to fit a suite of environmental variables to a NMDS using envfit(). Should I first exclude those environmental variables that are correlated? Should I then ...
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46 views

Interpreting results of ANOSIM conducted on non-abundance data

I am trying to understand how to implement and interpret an analysis of similarities (using the vegan package in R) in the following situation. Consider the following data frame: ...
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1answer
53 views

Clarification of methods for using non-parametric tests to compare groups- vegan package

I would like to validate my approach to comparing groups using non-parametric tests. data created below describes the structure of my data. Each ...
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51 views

Confusing F and p values in Two-way Permanova output

I am using 'adonis' from the vegan package in R to perform a permanova on butterfly species composition in tropical forest. I have two independent variables: Habitat (Undisturbed, Logged, Burnt) and ...
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2answers
313 views

Use vegdist function before metaMDS?

I am trying to do calculate beta-diversity of bacterial community data. I have been following numerous tutorials regarding this subject and I am getting mixed advice. I am trying to calculate beta-...
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How to control for group membership in multivariate community analysis (CCA) when group is confounded with explanatory variables of interest?

I am studying differences in microbiome composition across 11 different populations and attempting to identify correlations between microbiome community beta diversity and population-level covariates. ...
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1answer
380 views

In VEGAN ADONIS, what does "method='bray' do when I pass in a distance matrix I already have (UNIFRAC)?

Suppose I have a distance matrix created by applying the weighted unifrac measure. For instance, using a phyloseq object: ...
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1answer
101 views

WA site scores in dbRDA

I am working on a project trying to investigate differences in Bray-Curtis Dissimilarity (BCD) between 2 areas. There are 5 replicate samples in each area and 5 years of data. I also have a suite of ...
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1answer
341 views

What Null hypothesis does vegan::anova.cca(by = “terms”) test against?

I ran a distance-based Redundancy Analysis with the vegan R-package. Statistical significance of axes and explanatory variables can be tested with the anova.cca() function. Form Legendre et al. ...
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1answer
104 views

Correlation between constrained and unconstrained ordination axes

I am comparing several attributes between two types of things. My goals are (1) hypothesis testing and (2) to summarize the information from multiple attributes. PCA is an option, but this method is ...
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1answer
289 views

odd insignificant results using pairwise.perm.manova

I am trying to complete pairwise comparisons of 9 forest communities. Communities were significant at p < 0.001 using adonis. However, when I use the same bray curtis matrix with the pairwise.perm....
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1answer
301 views

R: Statistically testing NMDS community differences

Situation I am comparing species communities at 6 different sites. Communities at each site were measured repeatedly over 5 years. I used NMDS plots, based on bray-curtis distance matrices using ...
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104 views

Evaluating ecological community over time with NMDS?

I have sampling data of insect communities per month for 7 months. The sampling occurred in the same location with the same methods once a month. I want to be able to see community changes over time ...
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69 views

Comparing species correlations between species in two habitats

I have two community data sets (samples as rows, species as columns, populated with abundance). This data comes from two habitats/sites, with differing numbers of samples at each site. What I want ...
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103 views

Variation partition analysis: morphology-climate correlation, controlling for geography

I'm working with three datasets with informations about individuals: morphological data, climatic data of the individual sampling site and geographical data. My objective is to assess whether ...
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1answer
435 views

RDA and CCA output- unconstrained inertia 0.00 rank 0

I get an ouput for RDA and for CCA that says that my unconstrained inertia is 0, rank 0. I thought that would be a good thing, meaning that all the variance in the data is explained by my (constrained)...
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269 views

What do standard deviation ellipses mean in an ordination plot?

When kind = 'sd, ordiellipse() draws a single ellipse representing the "standard deviation' around each cluster in an ordination ...
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1answer
440 views

Can you use bray-curtis distances to evaluate standardized abundances in an NMDS?

So I'm trying to run an NMDS (using the vegan package in R) for a species X site matrix. Unfortunately the abundances of species are not inherently equal (If you can use that word) meaning that not ...
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724 views

How to code a model with the adonis function in R (permanova) for a paired/matched design (epidemiology study)

We have a database of 100 children that are grouped in 50 paired/matched groups (of 2 children) based on co-variables such as sex, c-section, and antibiotic treatments. We obtained the gut microbial ...
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1k views

R vegan: RDA vs CCA, which test to answer my research question and which results to report?

(if my question should be cut up into sub-questions please let me know, since all those questions are related I decided to ask them here together as one long question) Main question As part of my ...
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2k views

Is Hellinger transformation suitable to access species abundance - environmental variable relationships?

While working with a multivariate dataset, I noticed that Hellinger transformation reveals relationships with the dataset I did not see otherwise. The fact that a transformation affects species ...
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286 views

Can I use parametric and non-parametric tests in the same publication?

I have a rather difficult dataset. One measurement is non-normal and zero-inflated and could not be transformed to normality. Thus, a glm was used. Another set of ...
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1answer
168 views

Are NMDS Axis the same calculated for one or more dimensions?

I used NMDS axes of an ecological community as proxys for the community similarity in the different samples. I would like to "quantify" the importance of the different NMDS axis according to the ...
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1answer
1k views

Stress values of an nMDS analysis and p-values of ordisurf()

I have run a nMDS analysis in vegan and I have a few questions on the stress values of the analysis as well as the p-values associated with utilizing the ordisurf() function (also in vegan). First of ...
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227 views

Test for heteroscedasticity of continuous variables in R similar to betadisper()?

Before using adonis() with factors as explanatory variables in R, it is important to check for group dispersion (betadisper()) so that you know whether your significant p-value from adonis is real, i....
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1answer
587 views

Appropriate PERMANOVA (adonis) call for Subject Identity? (Terms drop in output)

I am working with a dataset of microbial species abundances at time points (baseline, 8h, 24h, 48h, 72h, 96h, 120h) for 23 subjects and have weighted unifrac, unweighted unifrac, and Bray-curtis ...
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1answer
1k views

What is the reason behind the name “adonis” (for permutational MANOVA)?

Does any one know why Permutational Multivariate Analysis of Variance Using Distance Matrices (PERMANOVA) is also called adonis? See https://www.r-bloggers.com/adonis-permanova-assumptions or http://...
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231 views

How to perform CCA with block design in R

Following example and data are completely fabricated: Suppose I am studying grooming behaviour in apes. I have four cages, 8 apes in each (4 females + males). For 24 hours I did an observations with ...
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1answer
3k views

Betadisper is significant, can I still do ADONIS and ANOSIM?

I'm a grad student in microbial ecology and I'm comparing some bacterial communities in experimental man made ponds. I've run the PCoA, NMDS, and CCA to see how various variables effect or influence ...
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1answer
5k views

adonis in vegan: order of variables — non nested with one degree of freedom for each

I am trying to understand why the order of variables seems to effect p values for both of those variables for the adonis() (Permutational Multivariate Analysis of ...
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1answer
685 views

Can MDS coordinates be used as variables in further analyses?

I have calculated an NMDS from vegetation community data taken from two habitat types using the metaMDS() function in vegan. My ...
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196 views

Should functional groups' abundances be transformed before using RDA?

I want to run Redundancy Analysis (RDA) with the abundance of different functional groups of plants (7 groups in total: shrubs, coniferous, forbs, etc.) as my response variables. I know that, for ...
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372 views

Should PERMANOVA be used to select factors for Canonical Correspondence Analysis?

I am interested in investigating the relationship between species composition and several environmental factors. My question is whether it is appropriate to use PERMANOVA to select a 'best' ...