Community Matrix and Analysis

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The workflow converts the LifeWatch dataframe format into a community matrix (site*taxa) for each selected location/groups of locations, finally processes community matrices. Several typologies of community composition analysis can be performed:

  • Species rarefaction curve: number of taxa~sample size rarefaction curve.

  • NMDS: 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.

  • Cluster analysis: hierarchical cluster analysis on a set of dissimilarities and methods for analysing it

  • Beta diversity: beta diversity according to Koleff et al. (2003)

  • Distance matrix: cross-site matrix of distances in community compositions

The dataset fields density and biovolume/biovolumeliter or carboncontent/carboncontentliter are mandatory and can be computed by the dedicated LifeWatch script (Traits Computation) or provided otherwise. 

Input values are:

  • Dataset: (LifeWatch Dataset): dataset with individual or aggregated records, Lifewatch format. The workflow runs only with data resources structured according to the LifeWatch Data Schema.  You can upload your file.

  • Cluster: level of aggregation for taxa selection. The aggregation could be done at spatial (i.e. ‘parenteventid’, ‘eventid’, ‘locality’, ‘country’) and/or temporal (i.e. ‘day’, ‘month’, ‘year’) levels. If cluster=NULL, the selection will be made on the whole dataset. 

  • SizeUnit: The measure to be considered for the ranked distribution, one amongdensity” (n of cells per liter), “biovolumeliter” (μm3 of cells per liter) or “carboncontentliter” (pgC per liter).

  • Taxonomic level : the taxonomic level at which the selection is made and the community matrix is build.

  • Analysis: analysis to be performed.

  • Method: method to calculate distances.

  • Display: one or both between ‘site’ and ‘species’ (analysis=‘nmds’) or one among ‘site’ and ‘species’ (analysis=cluster). Relevant if analysis = ‘nmds’ or ‘cluster’. Default=’site’.

  • Cex (between 0 and 50): size of graphical items. 

  • Type: plot type, text  or point. Relevant if analysis = ‘nmds’.

OUTPUT: a zip file with a matrix site*taxa file reporting the overall density (N of cells per liter) or the biovolume per liter (μm3 per liter) or carbon content per liter (pgC per liter), and a file representing the output of the analysis.

Select the input values and start the execution with the “Run the workflow” button.


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