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and Hydrology","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/FLARE-forecast/FLAREr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FLARE-forecast/FLAREr/actions/workflows/R-CMD-check.yaml)\n[![Codecov test coverage](https://codecov.io/gh/FLARE-forecast/FLAREr/branch/single-parameter/graph/badge.svg)](https://codecov.io/gh/FLARE-forecast/FLAREr?branch=single-parameter)\n\u003c!-- badges: end --\u003e\n\n# FLAREr\n\nThis document serves as a user guide and a tutorial for the FLARE (Forecasting Lake and Reservoir Ecosystems) system ([Thomas et al. 2020](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR026138)). FLARE generates forecasts with uncertainty of water temperature and water quality for 1- to 35-day-ahead time horizon at multiple depths of a lake or reservoir. It uses data assimilation to update the initial starting point for a forecast and the model parameters based a real-time statistical comparisons to observations.  It has been developed, tested, and evaluated for Falling Creek Reservoir in Virginia ([Thomas et al. 2020](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR026138)), Beaverdam Reservoir in Virginia ([Wander et al 2024](https://doi.org/10.1002/ecs2.4752)), Lake Sunapee in New Hampshire ([Woelmer et al. 2024](https://doi.org/10.1016/j.ecoinf.2024.102825)), National Ecological Observatory Network lakes across the United States ([Thomas et al. 2023](https://doi.org/10.1002/fee.2623) and [Olsson et al. 2024](https://doi.org/10.22541/essoar.171458144.44104603/v1)), and Lough Feeagh in Ireland ([Paíz et al. 2024](http://dx.doi.org/10.2139/ssrn.4888712)).\n\nFLAREr is a set of R scripts that\n\n* Generating the inputs and configuration files required by the General Lake Model (GLM)\n* Applying data assimilation to GLM\n* Processing and archiving forecast output\n* Visualizing forecast output\n\nFLARE uses the 1-D General Lake Model ([Hipsey et al. 2019](https://www.geosci-model-dev.net/12/473/2019/)) as the mechanistic process model that predicts hydrodynamics of the lake or reservoir. For forecasts of water quality, it uses GLM with the Aquatic Ecosystem Dynamics library. FLARE requires GLM version 3.3 or higher.\n\nMore information about the GLM can be found here:\n\n* [GLM 3.0.0 manuscript](https://www.geosci-model-dev.net/12/473/2019/) \n* [GLM on GitHub](https://github.com/AquaticEcoDynamics/glm-aed)\n* [GLM users guide](https://aquaticecodynamics.github.io/glm-workbook/) \n\nFLARE development has been supported by grants from the U.S. National Science Foundation (CNS-1737424, DBI-1933016, DBI-1933102)\n\n## Installation\n\nYou will need to download the necessary packages before running.\n\n```\nremotes::install_github(\"FLARE-forecast/FLAREr\")\n```\n\nNext, you need the GLM model.  You can get in using multiple pathways\n\nThe easiest way is to install the `GLM3r` package from Github using\n\n```\nremotes::install_github(\"rqthomas/GLM3r\")\n```\n\nor you can download it from the AquaticEcoDynamics GitHub organization.  This code assumes you are in the directory with the FLARE configurations and workflow subdirectories\n\n```\ndownload.file(\"https://github.com/rqthomas/glm-aed/archive/refs/heads/main.zip\", \"glm_aed.zip\")\nunzip(\"glm_aed.zip\")\n```\n\nif you are running on Mac you will need to run:\n\n```\nsystem2(\"chmod\",\"u+x glm-aed-main/binaries/macos/Sonoma/glm_latest/glm\")\nsystem2(\"./glm-aed-main/binaries/macos/Sonoma/glm_latest/glm\")\n```\n\nif you are running on Linux you will need to run:\n\n```\nsystem2(\"chmod\",\"u+x glm-aed-main/binaries/ubuntu/22.04/glm_latest/glm\")\nsystem2(\"./glm-aed-main/binaries/ubuntu/22.04/glm_latest/glm\")\n```\n\nWorking on windows\n\n## Use\n\nFLAREr is a set of functions that address key steps in the forecasting workflow. \n\n### Requires\n\nUser-generated *insitu* observations, meteorology, and inflow/outflow in a specified format.  See the FLARE example vignette for format specification.\nYou are required to set a directory structure as follows:\n\n\n\n### Quick Run\n\nThe code below will produce a single forecast for Falling Creek Reservoir using configuration files included with the package.\n\n```\nlibrary(arrow)\nlibrary(tidyverse)\nlibrary(FLAREr)\n\nremotes::install_github(\"rqthomas/GLM3r\")\nSys.setenv('GLM_PATH'='GLM3r')\n\n\ndir.create(tempdir(),showWarnings = FALSE)\nlake_directory \u003c- file.path(tempdir(), \"extdata\")\nfile.copy(system.file(\"extdata\", package = \"FLAREr\"), tempdir(), recursive = TRUE)\nrun_flare(lake_directory = lake_directory,configure_run_file = \"configure_run.yml\", config_set_name = \"default\")\n\nopen_dataset(file.path(lake_directory,\"forecasts/parquet\")) |\u003e \n  filter(variable == \"temperature\",\n         depth == 1) |\u003e \n  collect() |\u003e \n  ggplot(aes(x = datetime, y = prediction, group = parameter)) +\n  geom_line() +\n  geom_vline(aes(xintercept = as_datetime(reference_datetime))) +\n  labs(title = \"1 m water temperature forecast\")\n```\n\n\n\n \n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1002/ecs2.4752","https://doi.org/10.1016/j.ecoinf.2024.102825","https://doi.org/10.1002/fee.2623","https://doi.org/10.22541/essoar.171458144.44104603/v1","http://dx.doi.org/10.2139/ssrn.4888712"],"works":{"https://doi.org/10.1002/fee.2623":{"id":"https://openalex.org/W4363673287","doi":"https://doi.org/10.1002/fee.2623","title":"Near‐term forecasts of \u003cscp\u003eNEON\u003c/scp\u003e lakes reveal gradients of environmental predictability across the \u003cscp\u003eUS\u003c/scp\u003e","display_name":"Near‐term forecasts of \u003cscp\u003eNEON\u003c/scp\u003e lakes reveal gradients of environmental predictability across the \u003cscp\u003eUS\u003c/scp\u003e","publication_year":2023,"publication_date":"2023-04-09","ids":{"openalex":"https://openalex.org/W4363673287","doi":"https://doi.org/10.1002/fee.2623"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1002/fee.2623","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/fee.2623","source":{"id":"https://openalex.org/S144797041","display_name":"Frontiers in Ecology and the Environment","issn_l":"1540-9295","issn":["1540-9309","1540-9295"],"is_oa":false,"is_in_doaj":false,"host_organization":"https://openalex.org/P4310320503","host_organization_name":"Wiley-Blackwell","host_organization_lineage":["https://openalex.org/P4310320503","https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley-Blackwell","Wiley"],"type":"journal"},"license":"cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/fee.2623","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010063173","display_name":"R. 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