Phyto VRE Guide
In order to run the VRE and calculate phyto bioTraits (Biovolume, Surface Area, Surface Volume Ratio, Cells/Liter, Biovolume/Liter/Carbon Content and Carbon Content/Liter) and selection (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)) you should select your inputs that are:
- CalcType: the computation type. You can choose between two computation modalities:
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Simplified: it approximates the taxon specific-biovolumes calculation/computation based on two linear dimensions only, length and width. The mandatory fields for this calculation/computation type are scientific name, measurement remarks (e.g vision of the organism, dimension more or less than 20 μm), length and width;
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Advanced: it allows a more accurate estimate of taxon-specific biovolume, but it requires more information. For each shape, at least 2 measured basic linear dimensions need to be provided from. The mandatory fields for this calculation/computation type are scientific name, measurement remarks and linear dimensions. The latter must be measured according to the Phytobioimaging Atlas of Shapes (for more details, see here).
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- CompTraits: traits to be computed. You can choose among:
- Biovolume (BV);
- Surface Area (SA);
- Surface/Volume ratio (SV);
- Cells/Liter (CL);
- Biovolume/Liter (BVL);
- Carbon content (CC);
- Carbon content/Liter (CCL).
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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”). No default. The workflow runs only with data resources structured according to the LifeWatch Data Schema. You can select a Phytoplankton dataset from the list or upload your file.
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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. Default: c(parenteventid,eventid,locality, day, month,year).
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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).
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Taxlev : the taxonomic level at which the selection is made
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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.
OUTPUT: Two files: original dataset with individual records + one fields for each of the computed traits, called as the inputs of CompTraits. Original dataset excluding the taxa constituting less than the designated threshold of cumulative density/biovolume/biomass for each cluster of observations.