For each selected location/groups of locations, the script allows to exclude from the dataset rare taxa based on their rank distribution in density (n of cells per liter), biovolume per liter (μm³ of cells per liter) or carbon content per liter (pgC per liter). For any given sampling site and/or sampling time, the workflow also computes several community indices and/or individual size spectra statistics (biovolume in μm³ or biomass in pgC) from an individual or aggregated LifeWatch dataset. The fields density is mandatory and can be computed by the dedicated LifeWatch script (BiotraitsWorkflow) or provided otherwise.  If you don’t want to exclude rare records, please use threshold value =1. The inputs are: 

• Dataset: for entering data files in .csv format. The mandatory fields in the input dataset are scientific name, measurement remarks (e.g vision of the organism, dimension more or less than 20 μm), length and width (simplified calculation, see argument “CalcType”) or scientific name, measurement remarks and linear dimensions according to the Phytobioimaging Atlas of Shapes (advanced calculation, see argument “CalcType”). 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.  

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

• Taxlev: the taxonomic level at which the selection is made

• Threshold (between 0 and 1): threshold in the ranked distribution of taxa density/biovolume per liter/carbon content per liter above which taxa are retained in the dataset.

• Index: one or more among the different richness, diversity, evenness or environmental status indices available and/or statistics on the individual biovolume or biomass distribution.

  – Richness: Taxonomic Richness,
  – Diversity: Shannon, Shannon equivalents, Simpson, Simpson equivalents, Menhinick, Margalef, Gleason, McInthosh, Hurlbert
  – Evenness: Pielou, Sheldon, Ludwig-Reynolds
  – Dominance: Berger-Parker, McNaughton, Hulburt
  – Ecological status: Index of Size spectra Sensitivity of Phytoplankton, Diatoms-dinoflagellates ratio
  – Biovolume or Biomass Average, standard deviation, quantiles, interquantile and interdecile ranges of the biovolume (μm³) or biomass (pgC) distribution.

  OUTPUT: a zip wich contains a matrix (site*indices) with the calculated values and a barplot showing the indices distribution across sites.