Phytoplankton community analysis in the Northern Adriatic | Emodnet Biology

Phytoplankton community analysis in the Northern Adriatic

A workflow written in R, that gives a Multivariate representation of phytoplankton community in the LTER site in the Northern Adriatic.

Data series

The plankton series from the LTER site in the Northern Adriatic comprises three datasets in EMODnet biology: the phytoplankton series was started in 1986 and is continued until present. Results of the Microzooplankton series and Mesozooplankton series are available between 1998 and 2005.

  1. Link to dataset 1
  2. Link to dataset 2
  3. Link to dataset 3

Data  product

We show the evolution over time of depth-averaged abundance of major groups of species, as well as the most frequent species in the dataset. A frequency limit has been set to those species that have at least 20 occurrences during the course of the time series. The major groups are defined at the Class level, with few exceptions (Copepoda and Cirripedia are not Classes in taxonomic sense, but have been used as such). In the major groups, all species belonging to the group have been summed, also including the rare species that are not shown as separate species in the product.

In the Yearly series, we have averaged all data per year and present the results as box plots. When transformation is used (double square root transformation is offered), transformation has preceded the calculation of the box plots.

The Monthly series shows the average (over the years) monthly pattern of occurrence of the species or group. No distinction between several periods has been made.

the Multivariate representation of phytoplankton is based on a PCA of double square-root transformed species abundances of the most frequent species (the same species set that is shown in the time series). We present a biplot of samples and species, but we have grouped samples (and present centroids) in two different ways: per year and per season. This allows to show the long-term trend as a shift in yearly centroid (in red), and the seasonal fluctuation as variation between months (in blue). Both trends are at right angles in the biplot, suggesting little correlation between the seasonal and long-term fluctuations. The biplot further shows the species scores as arrows from the origin. The species selected and used to show yearly and monthly temporal variation, is/are highlighted in green in this graph. Upon selection of a new species, this highlighting is dynamically adapted. Thus, the multivariate graph shows how the selected species contributes to the temporal evolution of the community on long-term and seasonal scales

There is, as yet, no multivariate representation of microzooplankton or mesozooplankton composition. The field will be empty when a species in these groups is chosen.

R markdown

The application in R shiny


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