The scripts within this repository were used to standardize and compile a dataset of in situ chlorophyll-a data and related water quality data for lakes at or above 40° N across the Northern hemisphere. Original data files are not included, but can be found by following the links listed under "Data sources" below.
The period of chlorophyll-a increase (PCI) dataset contains the rate of chlorophyll-a increase along with mean water quality variables (i.e., surface water temperature, nutrients, and solar radiation) during periods of rapid algal growth referred to as the PCI. PCIs were defined based on the rate of change in the fluctuating chlorophyll-a concentration sampled over the year, and categorized as occurring in the spring, summer, or as a "single" PCI when there was one main period of growth. Additional lake parameters were included from the HydroLAKES and HydroATLAS databases, and trophic status index (TSI) was calculated from chlorophyll-a concentrations.
This dataset is intended to be used to explore trends between changing environmental conditions and lake productivity. However, as a compiled dataset, the PCI data is based on lake samples collected from a variety of organizations with differing methods. Great care was taken to standardize the data and provide all relevant metadata wherever possible. Therefore, it is recommended that the dataset be uniquely subsetted depending on the research question (e.g., for sampling frequency). The PCI dataset can be found in the FRDR repository, DOI:https://doi.org/10.20383/102.0488
To create the dataset, in situ lake physiochemical data and solar radiation data were collected from open source international, federal, and regional databases between May 2020 and January 2021. Original data files are not provided, but links to the data sources are listed below:
| Database | Region | Lake(s) | DOI | Data licence | Citation |
|---|---|---|---|---|---|
| Open Canada | Ontario | Laurentian great lakes | https://doi.org/10.18164/495eb10d-d423-432a-980f-264ef287d45b | Open Government Licence | |
| Open Canada | Ontario | Hamilton Harbour | https://doi.org/10.18164/05c4fa07-2a1e-46fa-a98a-1dc64bb97326 | Open Government Licence | |
| Open Canada | Manitoba | Riding Mountain lakes | Open Government Licence | ||
| Lake Winnipeg DataStream | Manitoba | Lake Winnipeg | Open Government Licence | ||
| CanWIN Data HUB | Manitoba | Lake Winnipeg | https://doi.org/10.5203/ywqt-vp63 | Open Data | Herbert, C., Stainton, T. (2019). CanWIN Lake Winnipeg to Lake Winnipeg Datastream Conversion, Version 1.0, Centre for Earth Observation Science. Winnipeg, MB: University of Manitoba |
| IISD-ELA private database | Ontario | Experimental lakes 114, 224, 239, and 442 | Terms and conditions | ||
| Alberta Environment and Parks data repository | Alberta | Many lakes sampled by Alberta Environment and Parks | Open Government Licence | ||
| LUBW data and map service | Germany | Constance Untersee | User agreement | ||
| National Institute for Environmental Studies Biodiversity Area | Japan | Kasumigaura | Terms of use | National Institute for Environmental Studies (2016) Lake Kasumigaura Database, National Institute for Environmental Studies, Japan. Accessed via https://db.cger.nies.go.jp/gem/moni-e/inter/GEMS/database/kasumi/index.html | |
| Water Information System Sweden (VISS) | Sweden | Many Lakes stored in the VISS database | CC0 license - free use | ||
| UK Environment Agency | UK | Many lakes monitored across the UK | Terms of use | ||
| UK Centre for Ecology and Hydrology | UK | Bassenthwaite | https://doi.org/10.5285/91d763f2-978d-4891-b3c6-f41d29b45d55 | Terms of use | Maberly, S.C.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G. ; Tanna, B.; Thackeray, S.J.; Vincent, C.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Bassenthwaite Lake, 1990 to 2013. NERC Environmental Information Data Centre. https://doi.org/10.5285/91d763f2-978d-4891-b3c6-f41d29b45d55 |
| UK Centre for Ecology and Hydrology | UK | Belhalm tarn | https://doi.org/10.5285/393a5946-8a22-4350-80f3-a60d753beb00 | Terms of use | Maberly, S.C.; Brierley, B.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G.; Tanna, B.; Thackeray, S.J.; Vincent, C.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Blelham Tarn, 1945 to 2013. NERC Environmental Information Data Centre. (Dataset). https://doi.org/10.5285/393a5946-8a22-4350-80f3-a60d753beb00 |
| UK Centre for Ecology and Hydrology | UK | Derwent water | https://doi.org/10.5285/106844ff-7b4c-45c3-8b4c-7cfb4a4b953b | Open Government Licence v3 | Maberly, S.C.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G. ; Tanna, B.; Thackeray, S.J.; Vincent, C.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Derwent Water, 1990 to 2013. NERC Environmental Information Data Centre. https://doi.org/10.5285/106844ff-7b4c-45c3-8b4c-7cfb4a4b953b |
| UK Centre for Ecology and Hydrology | UK | Esthwaite water | https://doi.org/10.5285/87360d1a-85d9-4a4e-b9ac-e315977a52d3 | Terms of use | Maberly, S.C.; Brierley, B.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G.; Tanna, B.; Thackeray, S.J.; Vincent, C.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Esthwaite Water, 1945 to 2013. NERC Environmental Information Data Centre. https://doi.org/10.5285/87360d1a-85d9-4a4e-b9ac-e315977a52d3 |
| UK Centre for Ecology and Hydrology | UK | Grasmere | https://doi.org/10.5285/b891c50a-1f77-48b2-9c41-7cc0e8993c50 | Terms of use | Maberly, S.C.; Brierley, B.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G.; Tanna, B.; Thackeray, S.J.; Vincent, C.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Grasmere, 1968 to 2013. NERC Environmental Information Data Centre. https://doi.org/10.5285/b891c50a-1f77-48b2-9c41-7cc0e8993c50 |
| UK Centre for Ecology and Hydrology | UK | Loch leven | https://doi.org/10.5285/2969776d-0b59-4435-a746-da50b8fd62a3 | Open Government Licence v3 | Dudley, B. J.; May, L.; Spears, B. M.; Kirika, A. (2013). Loch Leven long-term monitoring data: phosphorus, silica and chlorophyll concentrations, water clarity and temperature, 1985-2007. NERC Environmental Information Data Centre. https://doi.org/10.5285/2969776d-0b59-4435-a746-da50b8fd62a3 |
| UK Centre for Ecology and Hydrology | UK | Lake Windermere (north basin) | https://doi.org/10.5285/f385b60a-2a6b-432e-aadd-a9690415a0ca | Terms of use | Maberly, S.C.; Brierley, B.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G.; Tanna, B.; Thackeray, S.J.; Vincent, C.J.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Windermere North Basin, 1945 to 2013. NERC Environmental Information Data Centre. https://doi.org/10.5285/f385b60a-2a6b-432e-aadd-a9690415a0ca |
| UK Centre for Ecology and Hydrology | UK | Lake Windermere (south basin) | https://doi.org/10.5285/e3c4d368-215d-49b2-8e12-74c99c4c3a9d | Terms of use | Maberly, S.C.; Brierley, B.; Carter, H.T.; Clarke, M.A.; De Ville, M.M.; Fletcher, J.M.; James, J.B.; Keenan, P.; Kelly, J.L.; Mackay, E.B.; Parker, J.E.; Patel, M.; Pereira, M.G.; Rhodes, G.; Tanna, B.; Thackeray, S.J.; Vincent, C.J.; Feuchtmayr, H. (2017). Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Windermere South Basin, 1945 to 2013. NERC Environmental Information Data Centre. (Dataset). https://doi.org/10.5285/e3c4d368-215d-49b2-8e12-74c99c4c3a9d |
| Environmental Data Initiative portal | Global | Central long lake, East long lake, Giles lake, Lacawac, May lake, Paul lake, Peter lake, Tuesday lake, Waynwood lake, West long lake | https://doi.org/10.6073/pasta/6a658526e313dbcecbc0331a1f343c01 | Creative Commons license CC-BY 4.0 | |
| Knowledge Network for Biocomplexity (KNB) | Colerado | Oneida lake | Open Data Commons Attribution License | Lars G. Rudstam. Limnological data and depth profile from Oneida Lake, New York, 1975 to present. Knowledge Network for Biocomplexity. kgordon.35.96. | |
| University of Wisconsin NLTER | Wisconsin | Allequash lake, Big Muskellunge lake, Crystal lake, Crystal bog, Sparkling lake, Trout lake, Trout bog | https://doi.org/10.6073/pasta/6c8ee65f6876a7274bfe7714ae7c3a70 | Data use agreement | N. Lead PI, J. Magnuson, S. Carpenter, and E. Stanley. 2019. North Temperate Lakes LTER: Chlorophyll - Trout Lake Area 1981 - current ver 30. Environmental Data Initiative. https://doi.org/10.6073/pasta/6c8ee65f6876a7274bfe7714ae7c3a70. |
| University of Wisconsin NLTER | Wisconsin | Fish lake, Lake Mendota, lake Monona, Lake Wingra | https://doi.org/10.6073/pasta/f28e278afc34f1b7bd4f3cdc02b733a2 | Data use agreement | N. Lead PI, J. Magnuson, S. Carpenter, and E. Stanley. 2019. North Temperate Lakes LTER: Chlorophyll - Madison Lakes Area 1995 - current ver 27. Environmental Data Initiative. https://doi.org/10.6073/pasta/f28e278afc34f1b7bd4f3cdc02b733a2. |
| USGS and USEPA water quality | USA | USGS-491528094470601, USGS-492142094421501 | User guide |
| Database | Region | DOI | Data licence | Citation |
|---|---|---|---|---|
| ETH Zurich GEBA | Global | Data availability | ||
| Agriculture AB Station Data | Alberta | Terms of use | Data provided by Alberta Agriculture and Forestry, Alberta ClimateInformation Service (ACIS) https://acis.alberta.ca (August 2020) | |
| Baseline Solar Radiation Network | Global | https://doi.org/10.1594/PANGAEA.880000 | Creative Commons license CC-BY 4.0 | Driemel, A., Augustine, J., Behrens, K., Colle, S., Cox, C., Cuevas-Agulló, E., Denn, F. M., Duprat, T., Fukuda, M., Grobe, H., Haeffelin, M., Hodges, G., Hyett, N., Ijima, O., Kallis, A., Knap, W., Kustov, V., Long, C. N., Longenecker, D., Lupi, A., Maturilli, M., Mimouni, M., Ntsangwane, L., Ogihara, H., Olano, X., Olefs, M., Omori, M., Passamani, L., Pereira, E. B., Schmithüsen, H., Schumacher, S., Sieger, R., Tamlyn, J., Vogt, R., Vuilleumier, L., Xia, X., Ohmura, A., and König-Langlo, G.: Baseline Surface Radiation Network (BSRN): structure and data description (1992–2017), Earth Systems Science Data, 10, 1491-1501, doi:10.5194/essd-10-1491-2018, 2018. |
| Environment and Climate Change Canada (ECCC) | Canada | Source: direct communication with ECCC | Open Government Licence | |
| IISD-ELA private database | Ontario | Terms and conditions |
| Database | Description |
|---|---|
| Global Multi-resolution Terrain Elevation Data (GMTED2010) | Global digital elevation model used to extract lake and SSR station elevation in QGIS |
| HydroLAKES | Global lake shapefile used to assign lake area, mean depth, and volume |
| HydroATLAS | Global shapefile for regional attributes, used to assign climate zone to each lake |
PCIs are defined based on the normalized rate of change in chlorophyll-a concentration throughout the year after smoothing the annual time series for each lake using the Savitzky-Golay filter (Savitzky and Golay, 1964) and flagging optima in the smoothed data using the following functions:
Mean values were calculated for all water quality variables sampled during the growth window and are provided in the daily_mean.csv file.
Data files from varying sources were formatted to have consistent units and column headers; we removed all data recorded as below the instrument detection limit and selected years where samples were collected a minimum of 6 times over the year.
All data processing and analyses for this project were implemented using Python (ver. 3.7.6) and QGIS/PYQGIS (ver. 3.14).
Source files used to generate the PCI dataset
- lake_name_formatting.csv: conversion of lake names from original sampling location ID to name in the growth window dataset
- all_lake_coordinates.csv: list of coordinates for all lakes in the dataset, used in the PCI calculation scripts. Coordinates were collected from the original data files or searched within the database where possible, otherwise they were estimated based on sampling location name.
Scripts for formatting data and detecting PCIs
-
pci_functions.py: all functions used to generate the PCI dataset
-
pci_calculations.py: script used to call on the PCI functions
-
ssr_lakes_pairing_qgis.py: pairs lakes and SSR stations using PYQGIS
-
lake_dem_extraction.py: uses DEM in PYQGIS to extract lake elevation
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ssr_dem_extraction.py: uses DEM in PYQGIS to extract SSR station elevation
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paired_stations_ssr_calcs.py: calculates mean SSR during the PCI and pre-PCI period
subfolder: formatting_data:
Code used for initial formatting of raw data files before being read into the pci_calculations.py script
- one python file created for each lake or data source
This project is licensed under the Creative Commons Attribution 4.0 International license, please see CC BY 4.0 for details.
This work was funded by the Lake Futures project within the Global Water Futures (GWF) project supported by the Canada First Research Excellence Fund (CFREF). We would like to thank all the institutions and authors listed in the supplementary information for making their data open source and free to support our work.
Adams, H., Ye, J., Slowinski, S., Persaud, B., Kheyrollah Pour, H., van Cappellen, P. (2021). Rates and timing of chlorophyll-a increases and related environmental variables in global temperate and cold-temperate lakes. DOI:10.20383/102.0488.
Hannah Adams - Author - LinkedIn, GitHub, ORCiD
Jane Ye: - Co-author - LinkedIn
Hannah Adams - Author - LinkedIn, GitHub, ORCiD
Jane Ye: - Co-author - LinkedIn
Stephanie Slowinski: -Co-author - LinkedIn
Bhaleka Persaud: -Co-author - ORCiD
Homa Kheyrollah Pour: -Principle Investigator - Google Scholar, ReSEC lab
Philippe Van Cappellen: -Principle Investigator- Google Scholar, Ecohydrology Research Group, ORCiD