Oder Algae Bloom 2022 Spatiotemporal Chlorophyll and Discharge Analysis

About

This repository contains the code used to generate the spatiotemporal chlorophyll and discharge analysis for the 2022 Oder Algae Bloom.

Data

• The chlorophyll data is available in the data folder. (pixel_extraction_Oder_20220701_20220818_full_consolidated.txt)
• The river network data is available in the data folder.
• The discharge data has to be downloaded from Copernicus Climate Data Store (CDS) and is not included in this repository (data/discharge_{yyyy}_cropped.nc)
  • The data can be downloaded using the download.sh script.
  • Downloading the data requires an API key for CDS.
  • For downloading, the python version in pyenv has been used. It contains the packages cdsapi
  • There are issues with downloading cropped data so we have to download the full data and crop it manually. For cropping cdo is required.

Reproduce the analysis

Required Data

• Download the runoff data with data/download_discharge_data_full.sh
  • The required python package is cdsapi
  • You also require an API key for CDS.
  • Unzip the runoff data using unzip_discharge_data_full.sh
  • The data is quite large ~0.5TB after unzipping.
  • Crop the runoff data to size using crop_discharge_data_full.sh
  • requires CDO
• River network data can be downloaded from Inspire here.
• Chlorophyll data: data/chlorophyll_data.csv
  • Created by: Jorrit Scholze and Kerstin Stelzer, Brockmann Consult GmbH
  • License: The file data/chlorophyll_data.csv is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License http://creativecommons.org/licenses/by-nc/4.0/
• Measured discharge
  • data has to be requested (data/6030800_Hohensaaten-Finow_Q_TagWerte.csv and data/6030000_Eisenhuettenstadt_Q_TagWerte.csv): Department of Water Management 1, Brandenburg State Office for the Environment, 2022, Potsdam, Germany. Link: https://pegelportal.brandenburg.de.
  • License: https://www.govdata.de/dl-de/by-2-0
• City data
  • oder_cities.geojson and oder_towns.geojson.
  • Geographical location of relevant cities and towns.
  • Source: Open Street Map.
  • License: The files data/oder_cities.geojson and data/oder_towns.geojson are made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0/. Any rights in individual contents of the database are licensed under the Database Contents License: http://opendatacommons.org/licenses/dbcl/1.0/

Analysis

• See data/.gitignore for required files
• To reproduce the analysis compile map2wave_supplement.Rmd using the command

sh Rscript -e "rmarkdown::render('map2wave_supplement.Rmd')"

in the end of map2wave_supplement.html is a sessionInfo() output specifying all versions of R and R packages used

License

• The code in this repository is GPL v3 licensed, see the file [LICENSE](./LICENSE), datasets distributed with this repository have their own licenses, see Required Data for details.

Cite

Please cite as:

TODO!