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FLAREr

https://github.com/FLARE-forecast/FLAREr

Science Score: 59.0%

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    Found 13 DOI reference(s) in README
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    Links to: wiley.com
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    3 of 19 committers (15.8%) from academic institutions
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    Low similarity (14.6%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 8
  • Watchers: 3
  • Forks: 12
  • Open Issues: 5
  • Releases: 10
Created almost 6 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.md

R-CMD-check Codecov test coverage <!-- badges: end -->

FLAREr

This document serves as a user guide and a tutorial for the FLARE (Forecasting Lake and Reservoir Ecosystems) system (Thomas et al. 2020). 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), Beaverdam Reservoir in Virginia (Wander et al 2024), Lake Sunapee in New Hampshire (Woelmer et al. 2024), National Ecological Observatory Network lakes across the United States (Thomas et al. 2023 and Olsson et al. 2024), and Lough Feeagh in Ireland (Paíz et al. 2024).

FLAREr is a set of R scripts that

  • Generating the inputs and configuration files required by the General Lake Model (GLM)
  • Applying data assimilation to GLM
  • Processing and archiving forecast output
  • Visualizing forecast output

FLARE uses the 1-D General Lake Model (Hipsey et al. 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.

More information about the GLM can be found here:

FLARE development has been supported by grants from the U.S. National Science Foundation (CNS-1737424, DBI-1933016, DBI-1933102)

Installation

You will need to download the necessary packages before running.

remotes::install_github("FLARE-forecast/FLAREr")

Next, you need the GLM model. You can get in using multiple pathways

The easiest way is to install the GLM3r package from Github using

remotes::install_github("rqthomas/GLM3r")

or you can download it from the AquaticEcoDynamics GitHub organization. This code assumes you are in the directory with the FLARE configurations and workflow subdirectories

download.file("https://github.com/rqthomas/glm-aed/archive/refs/heads/main.zip", "glm_aed.zip") unzip("glm_aed.zip")

if you are running on Mac you will need to run:

system2("chmod","u+x glm-aed-main/binaries/macos/Sonoma/glm_latest/glm") system2("./glm-aed-main/binaries/macos/Sonoma/glm_latest/glm")

if you are running on Linux you will need to run:

system2("chmod","u+x glm-aed-main/binaries/ubuntu/22.04/glm_latest/glm") system2("./glm-aed-main/binaries/ubuntu/22.04/glm_latest/glm")

Working on windows

Use

FLAREr is a set of functions that address key steps in the forecasting workflow.

Requires

User-generated insitu observations, meteorology, and inflow/outflow in a specified format. See the FLARE example vignette for format specification. You are required to set a directory structure as follows:

Quick Run

The code below will produce a single forecast for Falling Creek Reservoir using configuration files included with the package.

``` library(arrow) library(tidyverse) library(FLAREr)

remotes::installgithub("rqthomas/GLM3r") Sys.setenv('GLMPATH'='GLM3r')

dir.create(tempdir(),showWarnings = FALSE) lakedirectory <- file.path(tempdir(), "extdata") file.copy(system.file("extdata", package = "FLAREr"), tempdir(), recursive = TRUE) runflare(lakedirectory = lakedirectory,configurerunfile = "configurerun.yml", configset_name = "default")

opendataset(file.path(lakedirectory,"forecasts/parquet")) |> filter(variable == "temperature", depth == 1) |> collect() |> ggplot(aes(x = datetime, y = prediction, group = parameter)) + geomline() + geomvline(aes(xintercept = asdatetime(referencedatetime))) + labs(title = "1 m water temperature forecast") ```

Owner

  • Name: FLARE-forecast
  • Login: FLARE-forecast
  • Kind: organization

GitHub Events

Total
  • Create event: 2
  • Issues event: 1
  • Release event: 2
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 29
  • Pull request event: 11
  • Fork event: 1
Last Year
  • Create event: 2
  • Issues event: 1
  • Release event: 2
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 29
  • Pull request event: 11
  • Fork event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 797
  • Total Committers: 19
  • Avg Commits per committer: 41.947
  • Development Distribution Score (DDS): 0.354
Past Year
  • Commits: 47
  • Committers: 5
  • Avg Commits per committer: 9.4
  • Development Distribution Score (DDS): 0.17
Top Committers
Name Email Commits
rqthomas r****s@v****u 515
tadhg-moore t****m@v****u 168
rqthomas r****s 43
Austin Delany a****y@g****m 28
Freya E Olsson f****o@t****r 9
Vahid Daneshmand v****d@g****m 8
tadhg.m t****e@d****e 6
LAPTOP-FO87M896\freya f****n@o****m 4
Freya E Olsson f****o@t****r 3
Freya E Olsson f****o@t****r 2
Freya E Olsson f****o@t****r 2
Freya E Olsson f****o@t****r 2
Cayelan Carey c****n@v****u 1
Freya E Olsson f****o@t****r 1
Freya E Olsson f****o@t****r 1
Freya E Olsson f****o@t****r 1
Freya E Olsson f****o@t****r 1
Freya E Olsson f****o@t****r 1
Quinn Thomas r****s@r****l 1
Committer Domains (Top 20 + Academic)
vt.edu: 3 tc255.cm.cluster: 1 tc192.cm.cluster: 1 tc070.cm.cluster: 1 tc054.cm.cluster: 1 tc006.cm.cluster: 1 tc041.cm.cluster: 1 tc035.cm.cluster: 1 tc016.cm.cluster: 1 tc100.cm.cluster: 1 dkit.ie: 1 tc063.cm.cluster: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 19
  • Total pull requests: 84
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 6 days
  • Total issue authors: 3
  • Total pull request authors: 7
  • Average comments per issue: 0.37
  • Average comments per pull request: 0.39
  • Merged pull requests: 80
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 15
  • Average time to close issues: 11 days
  • Average time to close pull requests: 5 days
  • Issue authors: 1
  • Pull request authors: 4
  • Average comments per issue: 0.25
  • Average comments per pull request: 0.13
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rqthomas (17)
  • vahid-dan (1)
  • melofton (1)
Pull Request Authors
  • rqthomas (38)
  • addelany (26)
  • tadhg-moore (17)
  • OlssonF (13)
  • Ashish-Ramrakhiani (8)
  • vahid-dan (2)
  • cayelan (1)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 14
proxy.golang.org: github.com/flare-forecast/flarer
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 1.6%
Average: 4.1%
Dependent packages count: 6.5%
Last synced: 9 months ago
proxy.golang.org: github.com/FLARE-forecast/FLAREr
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 9 months ago

Dependencies

.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • EML * imports
  • GLM3r * imports
  • dplyr * imports
  • emld * imports
  • ggplot2 * imports
  • imputeTS * imports
  • lubridate * imports
  • magrittr * imports
  • mvtnorm * imports
  • ncdf4 * imports
  • parallel * imports
  • patchwork * imports
  • plyr * imports
  • rMR * imports
  • readr * imports
  • stringr * imports
  • tibble * imports
  • tools * imports
  • yaml * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite