EMODnet-Biology-Phytoplankton-Interpolation

This directory provides the code for the reading of data files and performing spatial interpolation using DIVAnd software tool.

• Heatmap
• Neural network (binder does only provide 2GB of memory which is insufficient for this notebook)

Directory structure

{{EMODnet-Biology-Interpolated-Maps}}/
├── analysis
├── data/
├── docs/
├── product/
│   ├── figures/
│   └── netCDF/
└── scripts/

• analysis - Jupyter notebooks used to perform the data analysis, create the figures and the netCDF files.
• data - contains a text file with the URLs of the datafiles.
• docs - Rendered reports
• product - Output product files: netCDF containing the gridded, probability fields and the corresponding figures in PNG format.
• scripts - Reusable code: functions employed in the Jupyter notebooks.

Data

Data files have been produced by Deltares (Luuk van der Heijden, Willem Stolte).
They consist of CSV files containing the dates, coordinates and occurences (presence of absence) of 200 species in the North Sea.
The content of a data file looks like this (example for Gymnodinium-1995-2020.csv):

"abbr","date_year","genus","date_xUTM_yUTM","date","xUTM","yUTM","season","eventID","wint_year","occurs","gridnr","middleXgrid","middleYgrid"
"dome-phytoplankton",2010,"Gymnodinium","2010-01-11_477850.085718031_5756212.06783869",2010-01-11,477850.085718031,5756212.06783869,"winter",NA,NA,0,201,472500,5752500
"dome-phytoplankton",2010,"Gymnodinium","2010-01-11_560048.806065514_5746827.70084791",2010-01-11,560048.806065514,5746827.70084791,"winter",NA,NA,0,207,562500,5752500
"dome-phytoplankton",2010,"Gymnodinium","2010-01-11_563052.641129395_5744324.75671705",2010-01-11,563052.641129395,5744324.75671705,"winter",NA,NA,0,174,562500,5737500
"dome-phytoplankton",2010,"Gymnodinium","2010-01-11_742467.610873757_5940711.86346217",2010-01-11,742467.610873757,5940711.86346217,"winter",NA,NA,0,648,742500,5947500

Analysis

This directory contains the notebooks for the preparation and analysis of the data.

• emodnet_bio_DIVAndNN.ipynb: compute the probability map of phytoplankton in the North Sea using DIVAnd and a neural network.

• heatmap_testcase.ipynb: several simple test cases to illustrate how the probability is derived from heatmaps.

• interp_presence_absence.ipynb: documented application showing the interpolation of a single species: Biddulphia Sinensis.

• interp_presence_absence_prod.ipynb

• plot_data_histograms.ipynb

• plot_validationscore_L.ipynb

Citation

Please cite this product as: A. Barth, Willem Stolte, C. Troupin & Luuk van der Heijden (2020). Probability maps for different phytoplankton species in the North Sea.