Questions tagged [vegan]

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

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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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324 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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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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220 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
31 views

Measuring variation explained in community matrix using both geographic distance and and environmental variables

So I have this dataset where I have species community data from a variety of sites. I’m trying to explain what are the factors that drive the variation in these data. For each site, I have a ...
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81 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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187 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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544 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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1answer
147 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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157 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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279 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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188 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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232 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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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
74 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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139 views

Non-metric multidimensional scaling, no convergence

I'm using MetaMDS from the VEGAN package to run a non-metric multidimensional scaling analysis. My stress level for 3 dimensions is in the excellent range (i.e., stress<.05), however, the model ...
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1answer
128 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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62 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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1answer
145 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 ...