VEGAN, a package of R functions for community ecology

By Philip M. Dixon. 2003

6,049 citations recorded by the source corpus.

Subfields: Ecological Modeling, Ecology, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/30a9644bdaac6f0ca78e8f0cd6b5a23d37a4d006

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In Ecological Modeling

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Citations in the corpus

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis (2014, methodology): “Another commonly used transformation in 16S rRNA gene sequencing is the Hellinger transformation [43] implemented in the VEGAN R package [44].”
Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice (2016, methodology): “Vegan (60) was used to calculate the Simpson’s alpha diversity in each sample based on the relative abundance of each genus.”
A plant economics spectrum in Mediterranean forests along environmental gradients: is there coordination among leaf, stem and root traits? (2016, positive): “All these analyses were conducted in the R 2·10·0 statistical platform (R Development Core Team 2011), using the packages “ape” (Paradis et al. 2004), “car” (Fox & Weisberg 2011), “FactoMiner” (Lê et al. 2008), “phytools” (Revell 2012), “smatr” (Warton et al. 2012) and “vegan” (Dixon 2003).”
Enterotypes of the human gut mycobiome (2022, methodology): “…ASVs. α - and β -diversity analysis was conducted on samples at the sampling depth of 10,000 by utilizing the R packages “vegan” (version 2.5–7) [65] and “phyloseq” (version 1.34.0) [66]. α -diversity was estimated by the Shannon index (evenness and richness of community within a sample),…”
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem (2014, methodology): “and PERMDISP, were carried out with the Vegan package in R (62).”
Variation in forest soil fungal diversity along a latitudinal gradient (2013, methodology): “org/) (Dixon 2003).”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, methodology): “Statistical analyses can be carried out using the same software packages associated with R statistical software which possess a very diverse set of sub-programs, including ‘vegan’ or ‘Bioconductor’ (Dixon, 2003; Huber et al., 2015; Team, 2013).”
Molecular ecological network analyses (2012, methodology): “The Mantel tests were performed using the programs available in R vegan package [101].”
Marine DNA viral macro- and micro-diversity from pole to pole (2019, methodology): “The macrodiversity a- (Shannon’s H) statistics were performed using vegan in R (Dixon, 2003).”
Comparative analysis of diversity and environmental niches of soil bacterial, archaeal, fungal and protist communities reveal niche divergences along environmental gradients in the Alps (2021, methodology): “(Team, 2013), primarily using the phyloseq (McMurdie and Holmes, 2013) and vegan packages (Dixon, 2003), and visualised using ggplot2 (Wickham and Wickham, 2007).”