Questions tagged [vegan]

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

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What is postMDS doing?

I am trying to get a better understanding of what the postMDS function in R's vegan package is actually doing. I tried reading the documentation, but am having a hard time understanding it. I also ...
Philippa Richter's user avatar
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PERMANOVA with vegan (adonis) for three factors and repeated measures?

I have three factors (Status, Time.Point, Treatment) each with 2 levels. Time.Point factor is "before" and "after" (the repeated measures). The data is unbalanced though (e.g. some ...
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How to compare two species community matrices that were measured differently

I have two species community matrices, where each row is a site and each column is a species. The rows and columns are the same for each matrix (i.e., row 1 = site 1, column 1 = species A for both ...
aeiche01's user avatar
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PERMANOVA to calculate cytokine variation explained by species composition

I am trying to calculate the cytokine variation explained by species composition within my data set based on figure 2D in the following paper (Schirmer, M., Smeekens, S.P., Vlamakis, H., Jaeger, M., ...
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NMDS with ecological data containing many zeros in R - data transformations

I am trying to perform NMDS metaMDs() on mixed taxonomic data in R. My taxa data is organized with rows as observations and columns as different taxa. These data ...
Michael 's user avatar
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SIMPER results interpretation

I am doing a SIMPER analysis(R::vegan) where I want to determine which species are contributing the most to differences between thermo groups-warm and cold. (I am count data that is separated by years....
user390865's user avatar
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Which dissimilarity index to use with categorical ecological data

I am currently working on data representing the abundance of microorganisms in a categorical way, like 0 = no organisms; 1 = 1-5 organisms; 2 = 6-10 and so on (5 being the highest number). And i am ...
Fabi B's user avatar
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Why don't vegan::vegdist and vegan::metaMDS produce equivalent results?

This question has been discussed before but the proposed solution (https://stats.stackexchange.com/a/459820/170801) is no longer reproducible for some reason. As a refresher - it has been suggested ...
befriendabacter's user avatar
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Interpretation of R2 from PERMANOVA (adonis2) in vegan package

I am unclear on how the R2 output from adonis2 is interpreted. Is it that a particular factor "explains" the differences in community composition? And thus, would R2 be interpreted as ...
ecology's user avatar
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Plotting PCA cordinates as composites of environmental parameters into NMDS ordination of species assemblages

I have conducted a PCA and identified that the principal components (PC) are not driven by a single environmental parameter but are affected by several for each PC. I was then advised to retrieve the ...
user387025's user avatar
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Why am I seeing a low F-statistic, but a very significant p-value in permanova?

So I am having some numbers which I can't understand...basically I am performing a permanova test using the adonis2 function, from the vegan package, and what I see ...
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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 ...
amandarwills's user avatar
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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 ...
planktonQ's user avatar
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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 ...
planktonQ's user avatar
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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 ...
alexandradevon's user avatar
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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 ...
theforestecologist's user avatar
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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 ...
planktonQ's user avatar
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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 $...
planktonQ's user avatar
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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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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 ...
Joshua Smith's user avatar
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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 ...
Michael Dorman's user avatar
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1 answer
102 views

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. ...
Thomas's user avatar
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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 ...
aeiche01's user avatar
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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...
Jaynes01's user avatar
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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 ...
Sitta's user avatar
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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 ...
gabt's user avatar
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4 votes
2 answers
241 views

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 ...
Franc's user avatar
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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 ...
Valentine Reiss-Woolever's user avatar
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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 ...
Joshcole2504's user avatar
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1 answer
325 views

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 ...
Jincheng Wang's user avatar
1 vote
1 answer
681 views

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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1 vote
2 answers
3k 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 ...
wesleysc352's user avatar
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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 ...
Hugo Sentenac's user avatar
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1 answer
495 views

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 ...
Coldgrad's user avatar
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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 ...
Tim's user avatar
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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 ...
user340096's user avatar
1 vote
1 answer
345 views

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 ...
Jacob Weverka's user avatar
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2 answers
758 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 ...
slicer's user avatar
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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 ...
user257053's user avatar
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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 ...
sawezo's user avatar
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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 ...
Leovar's user avatar
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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 ...
Vijay Ramesh's user avatar
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92 views

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 ...
Adrien's user avatar
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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) ...
T.Skretting's user avatar
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80 views

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 ...
user257053's user avatar
1 vote
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5k views

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 ...
plicht's user avatar
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236 views

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 ...
basto's user avatar
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1 answer
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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 ...
Valentin Lucet's user avatar