PCI dataset

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

Data sources

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:

Lake data

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

Solar radiation data

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

Additional parameters:

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

Methods

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.

Quality assurance

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.

Software and packages

All data processing and analyses for this project were implemented using Python (ver. 3.7.6) and QGIS/PYQGIS (ver. 3.14).

Repository directory

Folder 1: Supplementary data:

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.

Folder 2: code

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
ssr_dem_extraction.py: uses DEM in PYQGIS to extract SSR station elevation
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

Sharing and accessing the data

This project is licensed under the Creative Commons Attribution 4.0 International license, please see CC BY 4.0 for details.

Funding

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.

Recommended citation

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.

Authors

Scripts

Hannah Adams - Author - LinkedIn, GitHub, ORCiD

Jane Ye: - Co-author - LinkedIn

Manuscript