vegan statistics

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Protocols

vegan specifications

Information


Unique identifier OMICS_01523
Name vegan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.5-2
Stability Stable
Requirements
parallel, lattice, knitr, MASS, cluster, mgcv, permute(≥0.9-0), R(≥3.2.0), tcltk
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Jari Oksanen

Publication for vegan

vegan citations

 (704)
library_books

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum

2018
Microbiome
PMCID: 5952429
PMID: 29764499
DOI: 10.1186/s40168-018-0472-x

[…] lucose levels, insulin sensitivity and disposition index) was tested using linear regression with and without adjustment for pre-pregnancy BMI.Analyses of community structure were performed using the vegan R packages. The cross-sectional difference in community structure between women with and without GDM and between women with GDM diagnosed by either fasting or stimulated hyperglycaemia or a comb […]

call_split

Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice

2018
PMCID: 5949713
PMID: 29760543
DOI: 10.3748/wjg.v24.i18.1995
call_split See protocol

[…] CH v9.2.64 package. For OTU clustering a threshold of 97% similarity was used through the UPARSE-OTU algorithm. α- and β-diversity analyses were calculated using the R package Phyloseq v.1.19.1[] and vegan 2.4_2 packets, using the OTU table normalized to the smallest sample size. Taxa with differential abundance between groups were identified using the Kruskal-Wallis test (P < 0.05). In the bar pl […]

call_split

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens

2018
Microbiome
PMCID: 5948730
PMID: 29753324
DOI: 10.1186/s40168-018-0477-5
call_split See protocol

[…] arisons with analysis of similarity percentages (SIMPER) [] was used to determine the contribution of each taxonomic unit to the Bray-Curtis dissimilarity of pairs of distinct sample groups using the vegan package [] in R using a script by Andrew Steinberger (https://github.com/asteinberger9/seq_scripts) as previously reported for the interrogation of 16S rDNA OTUs []. […]

call_split

Dissection of niche competition between introduced and indigenous arbuscular mycorrhizal fungi with respect to soybean yield responses

2018
Sci Rep
PMCID: 5943277
PMID: 29743529
DOI: 10.1038/s41598-018-25701-4
call_split See protocol

[…] y analysis of variance (ANOVA) with random effects for block differences were applied to evaluate the effects of the inoculation and P fertilizer application on shoot P concentration and grain yield. Vegan package for R was employed for β-diversity analysis with Bray-Curtis similarity index (read-abundance data based index) and for permutation multivariate analysis of variance (PERMANOVA) in which […]

library_books

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

2018
Front Microbiol
PMCID: 5938605
PMID: 29765359
DOI: 10.3389/fmicb.2018.00803

[…] ) distance matrices to test for differences in microbiome beta diversity between sample types, and tested for homogeneity of variance among samples using “betadisper” as implemented in the R package vegan (Oksanen et al., ). We visualized relative abundances of bacteria in paired sample types using the “plot_heatmap” function in phyloseq v. 1.22.3, and visualized ordination plots using Principle […]

library_books

Long term changes in the planktonic cnidarian community in a mesoscale area of the NW Mediterranean

2018
PLoS One
PMCID: 5929553
PMID: 29715282
DOI: 10.1371/journal.pone.0196431

[…] ing stations was performed. Species abundances were log (x+1) transformed and an ordination by a Bray-Curtis dissimilarity matrix was performed using the r-language function metaMDS available in the “vegan” package []. Subsequently, an adonis permutation multivariate analysis of variance and pairwise tests were used to test for significant differences in the cnidarian communities between surveys. […]

Citations

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vegan institution(s)
Department of Statistics, Iowa State University, Ames, IA, USA

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