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Community Matrix and Analysis

Home » Community Matrix and Analysis
The Community Matrix and Analysis web service allows users to create a community matrix from the input data file for each taxonomic, spatial and temporal level selected (site*time*taxa). Community matrices are by default created based on the trait Density, however the service also provides the computation of community matrices for Total Biovolume and Total Carbon content.
If the Density community matrix is selected the user can also perform the following analysis on it:
  • Species rarefaction curve: number of taxa~sample size rarefaction curve.
  • Beta diversity: beta diversity according to Koleff et al. (2003).
  • Distance matrix: cross-site matrix of distances in community compositions.
  • Cluster analysis: hierarchical cluster analysis on a set of dissimilarities and methods for analyzing it.
  • Nonmetric Multidimensional Scaling (NMDS): by attempting to find a stable solution using several random starts. In addition, it standardizes the scaling in the result, so that the configurations are easier to interpret, and adds species scores to the site ordination.

The web service will return a .zip file containing a community matrix (site*time*taxa) in .csv format and, if the Density community matrix is selected, also a .pdf file providing the graphical output of the selected analyses.


The mandatory fields for the community matrix and analyses are Density or Total Biovolume or Total Carbon Content. If these mandatory fields are not present in the dataset, they can be obtained by using the dedicated Traits Computation web service.


Please, follow the operational steps to run the service:
Please, specify all required values to run the service:
  • dataset
  • trait
  • taxonomic level
  • spatial and temporal levels
Please, specify all required values to run the service:
  • dataset
  • trait
  • taxonomic level
  • spatial and temporal levels
  • type of analysis

Please, specify the CEX value if you are selecting “Rarefaction” or “Betadiversity” as analysis type.

Please, specify all required values to run the service if you are selecting “NMDS” as analysis type:
  • cex value
  • analysis method
  • type
  • display type
Please, specify all required values to run the service if you are selecting “Distance” or “Cluster” as analysis type:
  • cex value
  • analysis method
  • display type

The CEX value value must be included between 0 and 50.

The CEX value must be numeric.

The input dataset must be a .csv file.

Step 1 – upload your dataset (*)

Upload your dataset structured according to the Phytoplankton Data Template.

Step 2 – select the trait (*)

You can select the trait to be used for the creation of the matrix:





Step 3 – select the taxonomic level (*)

You can select the taxonomic level to be used for the creation of the matrix.







Step 4 – select the spatial and temporal levels (*)

These levels are needed for the clusterization of data. If no spatial or temporal levels are selected, the distribution is made on the whole dataset.










Step 5 – select the type of analysis (*)

You can select the type of analysis to be performed on the Density community matrix.