Questions tagged [vegan]
R package for community and vegetation ecology. Includes ordination methods, diversity analysis, etc.
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Permutation design for repeated measures via how() in RDA
We would like to properly set up the permutation design in anova() testing for our rda().
Study design
We chose several areas, ...
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Why is the order of factors (order of samples in dataset) affect PERMANOVA results with adonis2?
I am trying to run PERMANOVA tests on multiomics datasets collected from coral samples using adonis2 (v 2.6-5). I found when the order of samples in my dataset change, the pvalues change, sometimes ...
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Are negative t-values important for pairwise betadisper results?
I am running the betadisper() function from the vegan package for an analysis of multivariate homogeneity of group dispersions.
...
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What do the weights in the specaccum function actually do?
I am trying to create a species accumulation curve that accounts for different areas of each sample. For example, samples were obtained from different sized quadrats. I think the weights argument in ...
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How do I extract the extrapolation prediction when setting the gamma argument in the specaccum function?
I am trying to use the specaccum function from the R vegan package to develop species accumulation curves.
However, I am trying ...
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Interpreting results of the vegan anova.cca function
1st question here!
I've scoured the internet, including the vegan documentation, but am still confused about the meaning of the F versus ChiSquare values in the results of the anova.cca() vegan ...
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Formal way to test if a non-linear approach is necessary to correlating environmental variables to NMDS ordination axes?
I've got a follow-up question to this post regarding correlating [non-]linear environmental variables to NMDS ordination axes.
My original plan was to use function ...
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How do you use numPerms to get the total number of unique permutations for a PERMANOVA?
I am trying to calculate the number of unique permutations for a PERMANOVA using the R adonis2 function but I am getting stuck on defining my permutation scheme.
As ...
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How do I find the number of unique permutations for a PERMANOVA with an unbalanced design?
From the PRIMER manual (p. 28 about Monte Carlo permutations; http://updates.primer-e.com/primer7/manuals/PERMANOVA+_manual.pdf), the number of unique permutations for a PERMANOVA with $a$ groups and $...
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Weird Adonis2 output in R: by="Margin" results in a R2 of 0, F of -Inf, and no P-value for 1 factor
I'm running a PERMANOVA analysis using vegan's adonis2. I have (rarefied) fungal community data (18S sequencing) of 24 samples. As treatments I have subplot (1,2,3,...
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Cross correlation analysis on Bray-Curtis dissimilarity matrix with environmental variables
I'd like to use a cross correlation analysis to examine whether there are temporal lags between environmental factors and changes in ecological community structure, but I am not sure how to structure ...
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Trying to run mantel test on asymetric distance matrices.. ideas?
I am trying to compare distances matrices belonging to two species matrices. One is bacteria and the other is ectomycorrhizal fungi. Both species matrices were generated from the same plant roots ...
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Methods for meta-analyzing ecological community dissimilarity matrices
What would be an appropriate method for meta-analyzing a set of five ecological dissimilarity matrices to generate an overall 'pooled' effect size? I have five ecological monitoring datasets that each ...
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Post-hoc pairwise comparison in `anova.cca` (package `vegan`)
Is there a way to perform a post-hoc pairwise comparison following anova.cca, for categorical independent variables with >2 levels, in the same sense as ...
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Find p-values from varpart table in vegan package
I have conducted a variance partitioning in R with the vegan package to test how weather variables partition in the variance of the green-up day.
...
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Accounting for 0 observations in presence/absence community data, PCoA/PCA: is this idea credible?
I have a solution in mind for this problem, but I'm not sure if it is defensible (which is why I'm asking you all!). I have a data frame where each row represents an individual site, each column ...
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How to perform a variation partitioning with random effects?
I would like to carry out a variation partitioning to see how weather and topography contribute to variation in the green-up day across states.
I would like to carry this out in R. My dataset is as ...
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repeated measures PERMANOVA nowhere to find
the internet seems full of people looking for a way to account for non-independence of samples when using the PERMANOVA method as implemented in the functions adonis...
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How to interpret angles between explantory variables in Redundancy analysis (RDA)?
I am learning to apply constrained ordination to community data using the vegan package in R. According to some materials, like this one, in a scaling type 2 RDA ...
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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 ...
Rachael Green
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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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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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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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863
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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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161
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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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428
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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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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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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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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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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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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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