JSNFRI, Japan Fisheries Research and Education Agency

On-line Analyses

• Diversity indices (species richness, Shannon, Simpson, and relative dominance) with their alpha, beta, and gamma by using an uploaded assemblage file: move to the analysis page
• nMDS ordination plot with K-medoid clusters by using an uploaded assemblage file: move to the analysis page

Analyses on Ecological Assemblages by R

Ecological assemblage data includes species composition (abundance or weight of species) at several sites. We would like to know diversity or similarity of assemblages. Several environmental factors are also measured at each site, to investigate relashionships with the assemblage. Multivariate techniques have been developed to analyze these data matrices.

In the web pages below, practical methods for multivariate assemblage analyses are explained with examples of R-codes.

• Diversity indices
  Renyi's diversity plofile shows a series of diversity indices. Diversity indices are interpolated or extrapolated over sample sizes.
• Unconstrained ordination
  Ordination plots of assemblages are constructed by nMDS and PCoA.
• Constrained ordination
  Effects of environmental factors on assemblages are analyzed by dbRDA.
• Cluster and Indicator species
  Assemblages are categorized by hierarchical or non-hierarchical clusters. Indicator species of these clusters are determined by IndVal.

Download sample data files below.

• Assemblage data file: spcdat.csv
• Environmental data file: envdat.csv

This page is a part of activities of "A feasibility study on biodiversity assessment methods in fishing ground environment" supported by the Fisheries Research Agency, Japan.