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Questions tagged [vegan]

vegan is a package for use with R for the analysis of ecological communities, especially vegetation communities. It has tools for analyzing ecological diversity and for the multivariate analysis of communities (NMDS, pCCA, pRDA, etc.)

Vegan is an package that provides ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Vegan contains many popular tools used in community ecology:

  • Diversity analysis: Shannon, Simpson, Fisher indices, Rényi diversities and Hill numbers.
  • Species abundance models: Fisher and Preston models, species abundance distributions.
  • Analysis of species richness: species accumulation curves, extrapolated richness.
  • Ordination: support and meta functions for NMDS, redundancy analysis, constrained correspondence analysis, constrained analysis of proximities (all three with partial analysis),
  • Support functions for ordination: dissimilarity indices, extended dissimilarities, Procrustes analysis, ordination diagnostics, permutation tests.
  • Ordination and environment: vector fitting, centroid fitting and smooth surface fitting, adding species scores as weighted averages, adding convex hull, SD ellipses, arrows etc. to ordination.
  • Dissimilarity analyses: ANOVA using dissimilarities, ANOSIM, MRPP, BIOENV, Mantel and partial Mantel tests.
  • Data standardization: Hellinger, Wisconsin, Chi-square, Beals smoothing.

Repositories

Vignettes

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partial Distance Based RDA - Centroids vanished from Plot

I am trying to fir a partial db-RDA with field.ID to correct for the repeated measurements character of the samples. However including Condition(field.ID) leads to Disappearance of the centroids of the main factor of interest from the plot (left…
Pharcyde
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vegan accumulation curve predictions

I'm having a matrix of plants(rows) and pollinators(columns) and interaction frequencies within (converted to 0 (no interaction) and 1 (interaction/s present) for this analysis). I'm using the vegan package and have produced a species accumulation…
AnkeS
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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 any way for make this possible? In my code: #1st…
Leprechault
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R vegan simper analysis: modify distance matrix

I am using a simper analysis from the Vegan package in order to determine which amino acid are responsible for the variation in protein composition between different samples. As I understood from this discussion, The simper() function uses…
Drosof
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Displaying a subset of Species in RDA plot in R based on variance explained

I've run an redundancy analysis on fish assemblage data using the rda() function from the vegan package in R. I'd like to only add species to the plot which had >10% of variance explained by the analysis. I have found a reference to doing that here…
wstiles
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Environmental Vectors to CCA plot in vegan (R)

I'm performing a constrained ordination in the vegan package using CCA function. I have a matrix of species composition at various sites and a related environmental matrix. invertcca<-cca(invert.rel~X100m, env) plot(invertcca) The default plot…
AquaticEcology
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RDA analysis in R gives error "attempt to set an attribute on NULL"

I'm running an analysis in R with the Vegan package. It's really simple in the way that I only want the summary to extract some values. But it keeps telling me an error message. Why? I have this dataset feed.raw1 =structure(c(0L, 0L, 2L, 0L, 0L,…
M. Beausoleil
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why it is "incorrect (no strata)" in adonis?

I am learning how to do PERMANOVA, it is really a challenge when I started from the example. The following code is from the help page in adonis. I can go through the example, but can't figure out why it is incorrect (no strata)? Does that mean I…
Ming
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"metaMDS" can do both PCoA and NMDS?

I am learning how to do PCoA, but when I test metaMDS, the result is different. NMDS<-metaMDS(eurodist) plot(NMDS) NMDS<-metaMDS(as.dist(eurodist)) plot(NMDS$points) http://www.davidzeleny.net/anadat-r/doku.php/en:pcoa_nmds this is where I…
Ming
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Error message when using Specpool in Vegan Package

I'm trying to calculate species richness and chao for a list of sites. However I keep getting this error message: Error in if (a2 > 0) var.chao[is] <- a1 * ssc * (0.5 + ssc * (1 + aa/4) * : missing value where TRUE/FALSE needed I'm not completely…
pr1g114413085
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DCA Vegan Small DCA1 Eigenvalues resulting in weird plot

Hello StackOverflow community, 5 weeks ago I learned to write and read R and it made me a happier being :) Stack Overflow helped me out a hundred times or more! For a while I have been struggling with vegan now. So far I have succeeded in making…
Erik Houtepen
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Rarefaction in specaccum producing errors for some data but not others of the same layout

I am trying to produce rarefied species accumulation curves for two different habitat types using the rarefaction method in specaccum function of the vegan package using the code: spa <- specaccum(Example, method = "rarefaction") The function works…
tom91
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rarecurve() plotted with Standard Error

Does rarecurve() (vegan) accept standard error for plotting? If so, how can I plot such a curve? I am following a classical script for this, with the BCI dataset: S <- specnumber(BCI) (raremax <- min(rowSums(BCI))) Srare <- rarefy(BCI,…
André Soares
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R Visualize cca plot in ggplot - Wrong arrows length

I am trying to customize a CCA plot performed in Vegan R package. I have used a benthic cover matrix (%) vs a fish abundance matrix (number of individuals) to run this analysis. I have collected data in 4 coral reefs in 2 years. I want to have the…
pedro_meirelles
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Test for richness accross samples with vegan

How can I test the differences between species richness (table below) using means (S.obs) and standard deviation (se.obs) with vegan or any other package in R? "Group.1" "S.obs" "se.obs" "Cliona celata complex" 499.7143 59.32867…
André Soares
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