Questions tagged [vegan]

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

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Permutation test for adonis under NA model?

I am having issues understanding why the permanova computed with adonis2() in vegan is returning a ...
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Constrained ordination (CAP) pairwise ANOVA

Is there any way to perform pairwise ANOVA test from Constrained ordination for multiple factors in a variable? e.g. I am trying to figure out whether microbial communities among five plant genotypes ...
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statistical significance after NMDS in r

I have performed an Non-metric multidimensional scaling (NMDS) to see if my two stations were different in terms of plankton abundances, using the metaMDS function in r (before I have performed a sqrt ...
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Spread of species and site scores in R (vegan) DCA ordination

I have performed a Detrended Correspondence Analysis on social survey answers, aiming to see the spread of answers to 25 interview questions and how they related to the three farmer types (n =45) we ...
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What is the appropriate way to statistically analyse diversity indexes?

I have been working with a soil-derived viral metagenomic data set and am looking for advice on the appropriate statistical approach to the results. I have 2 different sample areas. Within both areas ...
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betadisper with distance matrix or principle coordinates for ecological data?

When reading through the vegan::betadisper() function help document, I noticed that it is suggested that: "However, better measures of distance than the Euclidean distance are available for ...
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What does an r-squared of 1 mean for stress plot of NMDS analysis?

I'm doing a non-metric multidimensional scaling analysis. The analysis results in two convergent solutions and the output all look good, but when I made a stress plot to check the data I am getting an ...
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2 answers
258 views

In RDA redundancy analysis, what is the meaning of the principal components that appear in the result

I ran an RDA through the vegan package in R using water quality (dependent variable) and land use (independent variable) data. In my test I got the following ...
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Repeated measures Permanova and mean group differences for spectral data using PAVO and adonis function (vegan)

We are studying the iridescence (changes with viewing angle) of dorsal coloration in lizards. We took reflectance spectra at three different angles (0º, 60º, and 90º between illumination and viewing ...
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How to specify my permutation scheme?

I am studying the biofilm microbiome of mountain lakes and plan to use PERMANOVA with adonis2 to assess the importance of some grouping variables (e.g. lakes with introduced fish vs. lakes without ...
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1 answer
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What is a "permutation" in PERMANOVA?

I'm using PERMANOVA to calculate significant differences between groups in my beta-diversity analysis for 16S rRNA gene sequencing. However, while I understand the results, I don't understand what the ...
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231 views

Post-hoc test for PERMANOVA (adonis2) of a single variable (vegan package)

I have a 2x2 study design to test for the interaction between two drugs (i.e. with or without drug1 and/or drug2), with a single continuous outcome for each combination. The data are unbalanced and ...
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Dissimilarity only between different treatments in dataset

I am studying the impact of wildfires on vegetation species composition. I have surveyed the burnt and unburnt areas on six sites which burned at different points in time from which I now have species ...
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Variation partitioning using a large matrix as a predictor

I'm trying to understand the amount of variance explained in a univariate response using multiple community matrices as predictors. The problem is set up as such: I have the measured rate of a process ...
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1 vote
1 answer
181 views

Is adding a dummy value to the entire dataset correct way to deal with zero inflated Bray-Curtis Index in R (vegan/ Biodiversity) package?

I'm trying to calculate the "cproj" i.e. the projection values of each species using add.spec.score package in BiodiveristyR. My datapoints however are ...
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522 views

two-way PERMANOVA and violation of Multivariate homogeneity of groups dispersions

I would like to perform a two-way PERMANOVA for my data (n = 17; factor 1 with 2 factor levels, factor 2 with 3 factor levels and 20 continuous variables) using the vegan package. In order to ...
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GLM with temporal data where time is a factor and used in the y

looking for some help with how to correctly set up a GLM. I am quite new to the world of linear regression I have the following data ...
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Variable count in partial redundancy analysis

I am performing partial redundancy analysis in which I am trying to explain variation in Y with response to X after partialing out the impact of W. In this case, matrix W is a set of n-1 AEM spatial ...
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Investigate significance of adonis (Permanova) coefficients

Adonis' output for an analysis of multivariate variation between groups includes coefficients for all variables of the dataset. Is anyone aware of a way to ...
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Which NMDS axes should I plot?

I have been running some non-metric multidimensional scaling analysis on a bray-curtis dissimilarity matrix (using ecodist::distance()). Theory suggests that we ...
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Multivariate datasets comparison in R

I would like to compare the variance of two multivariate datasets describing the same population between them (e.g. Covariance) but also the specificity of one dataset regarding the total variance of ...
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How to account for spatial autocorrelation in adonis without using strata?

I am an undergrad student new to much of these stats. I am using NMDS ordination and Permanova testing to analyze variation in cover type (using count data) at different distance classes (0, 3, 10 m) ...
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PERMANOVA: removing dominant species to avoid dispersion effect

Dear StackExchange community, I have an ecological dataset that contains several species from different sample sites. One species is extremly abundant that contributes 80 - 90 % to the entire ...
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post-hoc (Tukey) on adonis (permanova) [closed]

I have a bray-curtis distance matrix and found significant associations on a grouping variable with adonis (permanova) using R package vegan. Now I would like to perfrom a post-hoc test to test ...
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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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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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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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183 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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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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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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2 votes
1 answer
615 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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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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7 votes
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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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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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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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2 votes
2 answers
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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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1 vote
1 answer
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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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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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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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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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1 vote
1 answer
531 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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1 answer
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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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3 votes
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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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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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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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1 answer
817 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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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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5 votes
1 answer
718 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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2 votes
1 answer
5k views

Can you perform a PERMANOVA analysis on nested data?

I've found no answer in the papers I have read regarding PERMANOVAs or on the web so I'm really hoping someone could help me answer this question. An example would be testing PERMANOVA on ...
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1 vote
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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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