Questions tagged [vegan]

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

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4 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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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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53 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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32 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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1answer
62 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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23 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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7 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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49 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
45 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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10 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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325 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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22 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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17 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
46 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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33 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
215 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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22 views

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
290 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
82 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
276 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
87 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
259 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
230 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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88 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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97 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
379 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 in the meaning that all the variance in the data is explained by my (...
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242 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
402 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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681 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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1answer
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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268 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
164 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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216 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
555 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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219 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
647 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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1answer
181 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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351 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' ...
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226 views

Specification of permutation design in RDA

I am using RDA to study plant communities in various land uses (variable LU with values M, U, etc.). For each land use, I sample 3 to 5 fields (M1, M2, U1, U2, etc). I make 5 measurements for both ...
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1answer
372 views

Calculation of the Shannon Index plotwise or over the entire population

Imagine I inventarized a forest with 28 plots. Do I calculate the Shannon-Index for each plot and take the average, or should I calculate the Shannon-Index over the whole population? I use R and the ...
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261 views

Residuals of symmetric Procrustes analyses are not symmetric

I am trying to replicate the analysis I saw in a paper. One of the step is to describe the relationships between two data tables. I use the procrustes() function ...
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1answer
277 views

Displaying large number of text labels on a scatter plot

Having too many species in the data, makes the species labels overlap in a plot of a canonical correspondence analysis. This makes it difficult to interpret. Is there a reasonable possible solution? ...
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113 views

Can I take an average of the values I got from Shannon-Weaver index?

Can I take an average of the values I got from Shannon-Weaver index ? OR Is it wrong to take an average of some values that we get after applying natural logarithm (ln) in an equation, like Shannon-...
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1answer
432 views

Variation partitioning in vegan. Do variables need to be centered?

I would like to carry out variation partitioning to see how landscape variables and local variables contribute to variation in species richness. Do I need to centre my data prior to analysis? ...