Questions tagged [vegan]
R package for community and vegetation ecology. Includes ordination methods, diversity analysis, etc.
105 questions
1 vote
2 answers
47 views
Using the residuals of a dbRDA analysis as a response in an adonis2 analysis?
I have ecological community data for about 100 sites across the United States, and a question I'm interested in is how and why these communities differ. To answer this, I've calculated taxonomic ...
- 13
0 votes
0 answers
69 views
How to test which variables to include in the adonis2 test?
I have been working on microbiome analysis data in R, vegan package. I want to be sure how to test which variables of my experiment should i include or not when performing the adonis2 test for beta ...
1 vote
1 answer
76 views
Comparing Shannon Diversity index with GLMMs?
I have a dataset comprised of species count samples across multiple years at different sites but within the same locality(same bay). The samples have been grouped into 2 categories based on the ...
- 93
1 vote
1 answer
58 views
Diversity statistics from standardised data
I have a dataset that includes both the raw counts of insects visiting a plant and the standardised counts of insects visiting per 100 flowers. The number of flowers per plants is somewhat comparable ...
- 11
2 votes
1 answer
197 views
Fixing rank deficiency model with glmmTMB?
I'm looking to find the effect of temperature on fish populations. I decided to use glmmTMB since there are random variables and works well with negative binomial model. I ended up needing to add a ...
- 93
0 votes
0 answers
62 views
Explaining PERMANOVA results(adonis function) compared to other multivariate tests?
I am using the adonis2 function to calculate PERMANOVA for two factors: temperature group and habitat on species composition. The results indicated both were ...
- 93
1 vote
2 answers
89 views
Does vegan's varpart() need gaussian distribution?
I am carrying out variation partitioning to find out which of my variables, soil volume (soil_vol) or carbon percentage in soil (...
2 votes
1 answer
93 views
Correct permutation design for envfit (nested study design)?
I have the following study design: 8 locations, 5 forest types/"stands" (Plots) per location (D,DB,B,FB,F). In every plot I sampled spiders and identified them. I did an 3 dimensional NMDS ...
- 69
1 vote
1 answer
194 views
Nested studydesign - Necessary to restrict permutations in betadisper?
I have the following study design: 8 locations, 5 forest types (Plots) per location (D,DB,B,FB,F). In every plot I sampled spiders and identified them. I did an NMDS with Morisita-Horn index. ...
- 69
0 votes
1 answer
136 views
test for significant differences in communtiy composition between habitats? required PERMANOVA sample size?
I sampled spiders in 5 different forest-stands. I originally had a sample size of 32 per forest-type, but as I had to pool the data I now just have 8 samples per forest type. I did an ordination with ...
- 69
0 votes
0 answers
75 views
Are fixed effects not being evaluated by the model?
I have a mixed effect model that includes some variables as fixed effects and some as random effects. All of them are defined as factors, and I set appropriate reference levels. ...
- 207
0 votes
0 answers
53 views
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 ...
3 votes
1 answer
1k views
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 ...
- 135
1 vote
2 answers
241 views
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 ...
- 117
1 vote
0 answers
51 views
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., ...
- 11