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and Hydrology","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\", echo = TRUE, warning = FALSE, message=FALSE\n)\n```\n\n# LakeEnsemblR \u003ca href=\"https://aemon-j.github.io/LakeEnsemblR/\"\u003e\u003cimg src=\"man/figures/logo.png\" alt=\"LakeEnsemblR website\" align=\"right\" height=\"120\"/\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/aemon-j/LakeEnsemblR/workflows/R-CMD-check/badge.svg)](https://github.com/aemon-j/LakeEnsemblR/actions) [![codecov](https://codecov.io/github/aemon-j/LakeEnsemblR/branch/master/graphs/badge.svg)](https://codecov.io/github/aemon-j/LakeEnsemblR/) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![DOI](https://zenodo.org/badge/217581132.svg)](https://zenodo.org/badge/latestdoi/217581132)\n[![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1016/j.envsoft.2021.105101)](https://juleskreuer.eu/projekte/citation-badge/)\n\u003c!-- badges: end --\u003e\n\nTools for running an ensemble of lake models using standardised input data. Lake models currently incorporated are [Freshwater Lake Model (FLake)](http://www.flake.igb-berlin.de/), [General Lake Model (GLM)](http://aed.see.uwa.edu.au/research/models/GLM/), [General Ocean Turbulence Model (GOTM)](https://gotm.net/) (lake-branch), [Simstrat](https://www.eawag.ch/en/department/surf/projects/simstrat/), and [MyLake](https://github.com/biogeochemistry/MyLake_public).\n\nYou can find example setups here: https://github.com/aemon-j/LER_examples.\n\nCheck out our published paper [LakeEnsemblR: An R package that facilitates ensemble modelling of lakes](https://doi.org/10.1016/j.envsoft.2021.105101).\n\nIn v1.1, some changes occurred in the configuration file. If you want to adapt your existing setup, see: https://github.com/aemon-j/LakeEnsemblR/wiki/From-v1.0-to-v1.1\n  \n\n## Installation\n\nPrior to installing the package, you will need to install the packages which run the models and the tools for manipulating model data from GitHub. It is recommended to do this each time before testing to ensure all packages are up-to-date as parallel development might be ongoing.\n\n``` r\n# install.packages(\"remotes\")\nremotes::install_github(\"GLEON/rLakeAnalyzer\")\nremotes::install_github(\"aemon-j/GLM3r\", ref = \"v3.1.1\")\nremotes::install_github(\"USGS-R/glmtools\", ref = \"ggplot_overhaul\")\nremotes::install_github(\"aemon-j/FLakeR\", ref = \"inflow\")\nremotes::install_github(\"aemon-j/GOTMr\")\nremotes::install_github(\"aemon-j/gotmtools\")\nremotes::install_github(\"aemon-j/SimstratR\")\nremotes::install_github(\"aemon-j/MyLakeR\")\n```\n\nFollowing this you can install `LakeEnsemblR` from Github with:\n\n``` r\nremotes::install_github(\"aemon-j/LakeEnsemblR\")\n```\n\nShould you run into unexpected installation issues, please have a look at this page: https://github.com/aemon-j/LakeEnsemblR/wiki/Installation-issues\n\n### Visualize\n\nYou can download [PyNcView](https://github.com/BoldingBruggeman/pyncview/releases/), a cross-platform NetCDF viewer, for viewing the NetCDF output.\n\n## Example model run\n\n```{r copy-files,echo = TRUE,result = \"hide\",warning = FALSE,message=FALSE}\n\n# Load LakeEnsemblR\nlibrary(LakeEnsemblR)\n\n# Copy template folder\ntemplate_folder \u003c- system.file(\"extdata/feeagh\", package= \"LakeEnsemblR\")\ndir.create(\"example\") # Create example folder\nfile.copy(from = template_folder, to = \"example\", recursive = TRUE)\nsetwd(\"example/feeagh\") # Change working directory to example folder\n\n```\n\n```{r, setup, include=FALSE}\nknitr::opts_knit$set(root.dir = \"example/feeagh\")\n```\n\n```{r run-LER,result = \"hide\",warning = FALSE,message=FALSE}\n\n# Set config file \u0026 models\nconfig_file \u003c- \"LakeEnsemblR.yaml\"\nmodel \u003c- c(\"FLake\", \"GLM\", \"GOTM\", \"Simstrat\", \"MyLake\")\n\n# Example run\n# 1. Export settings - creates directories with all model setups and exports settings from the LER configuration file\nexport_config(config_file = config_file, model = model)\n\n# 2. Run ensemble lake models\nrun_ensemble(config_file = config_file, model = model)\n```\n\n\n## Post-processing\n\n```{r post-process}\n\n# Load libraries for post-processing\nlibrary(gotmtools)\nlibrary(ggplot2)\n\n## Plot model output using gotmtools/ggplot2\n# Extract names of all the variables in netCDF\nncdf \u003c- \"output/ensemble_output.nc\"\nvars \u003c- gotmtools::list_vars(ncdf)\nvars # Print variables\n\np1 \u003c- plot_heatmap(ncdf)\np1\n# Change the theme and increase text size for saving\np1 \u003c- p1 +\n  theme_classic(base_size = 14) + \n  scale_colour_gradientn(limits = c(0, 21),\n                         colours = rev(RColorBrewer::brewer.pal(11, \"Spectral\")))\n\np1\n\n```\n\n## Plot Ensemble output\n\n```{r plot-ensemble}\n# Plot ensemble mean at 0.9m\nmodel = c(\"FLake\", \"GLM\", \"GOTM\", \"Simstrat\", \"MyLake\")\nplot_ensemble(ncdf = ncdf, model = model, var = \"temp\", depth = 0.9)\n\n# Load watertemp from netCDF file as a list\nwtemp \u003c- load_var(ncdf = ncdf, var = \"temp\", return = \"list\")\nnames(wtemp)\n\n# Plot residual diagnostic plots\nplots \u003c- plot_resid(var_list = wtemp) # Plot residuals - returns a list of plots\nnames(plots) #\n\n# Plot residuals vs. depth (\"res_depth\")\nplots[[2]]\n\n# Analyse the netCDF output\nout \u003c- analyse_ncdf(ncdf, model = model, spin_up = 0)\nnames(out)\nstr \u003c- out[[\"strat\"]]\nstr[str$year == 2010, ]\nstats \u003c- out[[\"stats\"]]\nstats\n```\n\nSee the [vignette](articles/lakeensemblr-overview.html) for further examples.\n\n\n# How do I setup `LakeEnsemblR` for my lake?\n\nHead on over to our [website](https://aemon-j.github.io/LakeEnsemblR/index.html) for guides on how to set up your lake for LakeEnsemblR\n\n# How do I contribute new code back to the `LakeEnsemblR` project?\n\nIn order to contribute to this code, we recommend the following workflow:\n\n1.  \"fork\" this repository to your own personal github account\n\n2.  clone the github repository to your computer:\n\n    $git clone \u003cgit@github.com:USER_NAME/LakeEnsemblR.git\u003e\n\n3.  modify code or add new functionality, save the code\n\n4.  add the repository master to a remote master called \"upstream\"\n\n    $cd LakeEnsemblR\n\n    $git remote add upstream \u003cgit@github.com:aemon-j/LakeEnsemblR.git\u003e\n\n5.  before pushing your changes to your repository, pull in the current version of the aemon-j master:\n\n    $git fetch upstream\n\n6.  merge these differences with your own \"master\" version:\n\n    $git merge upstream/master\n\n7.  push your changes to your github repository, in addition to changes made by pulling in the aemon-j master:\n\n    $git push\n\n8.  submit a pull request to aemon-j master using your account at github.com\n\n\n# Information for macOS users\n\nTo ensure that all model binaries work, we advise you to install the specific macOS packages (currently in a separated branch):\n```\nremotes::install_github(\"aemon-j/GLM3r\", ref = \"macOS\")\nremotes::install_github(\"aemon-j/FLakeR\", ref = \"macOS\")\nremotes::install_github(\"aemon-J/GOTMr\", ref = \"macOS\")\nremotes::install_github(\"aemon-j/SimstratR\", ref = \"macOS\")\n```\n\nUnfortunately, this means your version of GLM will differ compared to the one included in the executables for Windows and Linux. GLM on macOS will be version 3.2.0a8 (most recent one on January 13, 2022), Windows/Linux use 3.1.1. \n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1016/j.envsoft.2021.105101"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/324914","html_url":"https://ost.ecosyste.ms/projects/324914"}