Hydrodynamic and ensemble lake modelling

🗓️ October 13, 2022

⏰ 9:00-13:00

👥 Tom Shatwell (tom.shatwell@ufz.de), Karsten Rinke (karsten.rinke@ufz.de)

📄 OA journal article on the LakeEnsemblR R-package

Description

This training module will provide an introduction into lake hydrodynamic modelling. After a short introductory presentation we will apply the 1D lake model FLake to an example waterbody. After learning how to apply one hydrodynamic model, we will dive into ensemble modelling with the R package "LakeEnsemblR" that has been developed within the GLEON modelling group. Learn how to set up multiple lake models for your lake physical system, how to calibrate your models and explore model uncertainty.

What will this workshop cover?

Introduction to hydrodynamic modelling of lakes
Introduction to the FLake model
Introduction to LakeEnsemblR package:
- Why use ensembles?
- What is LakeEnsemblR?
Using LakeEnsemblR:
- Standardisation of input data
- Functions
- Visualising output & calibration
If you would like to model your own lake, you should gather the following data:
- Lake data like hypsographic / bathymetric information (depth vs area), extinction coefficient or Secchi depth, location (lat/lon)
- Meteorological data (shortwave radiation, air temp, humidity, wind, cloud cover, precipitation)
- (Optional) Inflow data (flow rate, inflow temperature, salinity if relevant)
- (Optional) Outflow data
- (Optional) Observed data (e.g. temperature profiles, ice, water level)
See the LakeEnsemblR vignette and the LakeEnsemblR examples for more deatiled information.

Prerequisites

1. Install the required software

In this workshop, you will need R (version>=3.5) and a GUI of your choice (preferably RStudio - desktop free version). You will also need a decent text editor (e.g. Notepad++) and netcdf viewer like PyNcView. Windows users can download PyNcView for example here. Linux users can install PyNcView via PyPi, then with the command pip install pyncview. Mac users, try to find a download on the web, or email me at tom.shatwell@ufz.de.

2. Set up the FLake hydrodynamic model

Clone or download files from this Github repository to a local directory on your computer. Keep the file structure as it is. That should be all you have to do!

Optional:

If you would like to compile the model yourself and have the gfortran compiler on your system, then follow these steps:

On your computer, navigate to /path/to/LakeEnsemblR_intro/flake/sources/ and then run the file "makeflake_win.bat" on Windows, "makeflake_linux.sh" on linux, or "makeflake_mac.sh" on macOS. This should create an executable file in the "sources" directory called flake.exe on win, nixflake on linux, or macflake on macOS.
Move the executable file you just created from the "LakeEnsemblR_intro/flake/sources" directory up one level to /LakeEnsemblR_intro/flake/ and replace the existing executable with the same name.

3. Set up the LakeEnsemblR R-package

This step can take a while, so rather do it in advance of the training. To set up LakeEnsemblR, first open R or your IDE like RStudio. Then install the "remotes", "ggplot2", "ggpubr" and "reshape" packages by entering the following commands into the console.

install.packages("remotes")
install.packages("ggplot2")
install.packages("ggpubr")
install.packages("reshape")

Next, install the specific LakeEnsemblR packages from github.

Windows and Linux users:

remotes::install_github("GLEON/rLakeAnalyzer")
remotes::install_github("aemon-j/GLM3r", ref = "v3.1.1")
remotes::install_github("USGS-R/glmtools", ref = "ggplot_overhaul")
remotes::install_github("aemon-j/FLakeR", ref = "inflow")
remotes::install_github("aemon-j/GOTMr")
remotes::install_github("aemon-j/gotmtools")
remotes::install_github("aemon-j/SimstratR")
remotes::install_github("aemon-j/MyLakeR")
remotes::install_github("aemon-j/LakeEnsemblR")

macOS users:

remotes::install_github("GLEON/rLakeAnalyzer")
remotes::install_github("aemon-j/GLM3r", ref = "macOS")
remotes::install_github("USGS-R/glmtools", ref = "ggplot_overhaul")
remotes::install_github("aemon-j/FLakeR", ref = "macOS")
remotes::install_github("aemon-J/GOTMr", ref = "macOS")
remotes::install_github("aemon-j/gotmtools")
remotes::install_github("aemon-j/SimstratR", ref = "macOS")
remotes::install_github("aemon-j/MyLakeR")
remotes::install_github("aemon-j/LakeEnsemblR")

Unfortunately, the macOS version of GLM will differ to the one included in the executables for Windows and Linux. GLM on macOS will be version 3.2.0a8 (most recent on January 13, 2022), Windows/Linux use 3.1.1.

4. Check that your setup is working

Open RStudio (for instance by double-clicking the file LakeEnsemblR_intro.Rproj), and then run the test script test_BEFORE_workshop.R.

If you ran the script to the end without errors, congratulations, everything looks good. If you encountered errors or encounter other problems, please get in touch by email.

Files

Workshop Files

The HTML and PDF files in the repository both contain the information needed for the workshop. You can pick which one you prefer. You can copy the code into an R script and run it yourself, or use the pre-made R script ("InventWater_LakeEnsemblR.R"), which contains all the lines of code that are run during the workshop and some short comments.

LakeEnsemblR Examples

There is a selection of lakes of different areas, depths and climatic zones that have been collated to show you different applications of LakeEnsemblR. They can be downloaded from the LER_examples repository on the "aemon-j" GitHub account.

Acknowledgement

The workshop material on LakeEnsemblR, including the nice presentation and structure in this github repo, was developed by the LakeEnsemblR core developers Jorrit Mesman, Johannes Feldbauer, Tadhg Moore, and Robert Ladwig. It was presented at GLEON21.5 in the GSA workshop series. We are very grateful for their help.

💻 Original LakeEnsemblR GSA workshop material

anandita473/LakeEnsemblR_intro