All Questions
Tagged with multivariate-testing vegan
14 questions
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1
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708
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Does PERMANOVA analysis (specifically adonis2 in the vegan package) allow for nested terms?
I am trying to run a PERMANOVA analysis on the bray-cutis dissimilarities between my samples, but I need to nest sample days within time of day. I read that the "strata" function in adonis2 ...
- 11
0
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1
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693
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PERMANOVA - unbalanced design
I am new to statistical analysis and R. I have data of relative abundance (in percentage) of 5 taxa in 8 ponds. The number of samples in the 8 ponds ranges from 7 to 12 (making the design unbalanced). ...
- 3
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1
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611
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RDA triplot in R- plot only numeric explanatory variables as arrows; factors as centroids
I ran a distance-based RDA using capscale() in the vegan library in R and I am trying to plot my results as a custom triplot. I only want numeric or continuous explanatory variables to be plotted as ...
- 13
1
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1
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360
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How can I change the colour of my points on my db-RDA triplot in R?
QUESTION: I am building a triplot for the results of my distance-based RDA in R, library(vegan). I can get a triplot to build, but can't figure out how to make the colours of my sites different based ...
- 13
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2
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989
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Why I having problem on assigning data for NMDS in R?
I want learn Non-matric multidimensional scale, I have these data downloaded from https://cougrstats.wordpress.com/2019/12/11/non-metric-multidimensional-scaling-nmds-in-r/
data are
library(vegan)
...
- 77
0
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0
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110
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Testing that an individual species in a matrix has a significant impact on the entire assemblage
I feel like this is kind of an elementary question but w/all my reading in and around the subject I have yet to arrive at a conclusive answer.
I'm testing an ecological (site*species) data set as part ...
- 13
1
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1
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1k
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In multivariate analysis using PERMANOVA and NMDS, is it appropriate to include both predictors in my model?
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) ...
- 13
0
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1
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3k
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R vegan: adjusted p values for permanova (adonis2)
I am running an analysis of variances on a large distance matrix using adonis2 as described here: https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/adonis
That method is frequently ...
- 113
1
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1
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3k
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Extract R2 values from multiple adonis results
I am wondering if there is some way how to extract results from adonis function in vegan package and possibly save it by write.table?
I mean other way than print results to console and copy-past R2 ...
user7886302
1
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1
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1k
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Alternative example for capscale function in vegan package
I have been learning multivariate analyses in PRIMER, yet now want to convert to R using the vegan package. I wish to use the capscale() function in vegan, yet am not sure how my data should be ...
- 4,309
0
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1
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249
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Joint plots with vectors from a subset of the data
I'm generating NMDS ordination plots from community data using the R package, vegan, and want to include vectors (ie arrows from the origin) whose lengths correspond to the importance of selected ...
- 85
0
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0
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392
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More then three independent contrasts in PERMANOVA
I try to create more then three independent contrasts in PERMANOVA with 4 factors without success. I need to use all possible pairwise combinations of factor levels in my contr2df object. There are ...
- 1,801
1
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1
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4k
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PERMANOVA multivariate spread among groups is not similar to variance homogeneity ANOVA
I try to understand a PERMANOVA assumtption that is multivariate spread among groups is similar to variance homogeneity in univariate ANOVA, for this I make a R code and I don't find this results, why?...
- 1,801
0
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0
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831
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Extract residuals from adonis function in vegan package
I am using the adonis function in the vegan package to determine effects of different environmental factors in forest plant community composition in different regions. I would like to first use adonis ...
