LakeEnsemblR.WQ: Calculate and Export Lake Ecosystem Metrics

This version of the package focuses on harmonizing and post-processing lake model outputs from GLM-AED2, GOTM-WET, and GOTM-SELMAPROTBAS. Using raw model outputs, the package calculates system metrics (as outlined in Hipsey et al. 2021) and returns them in a structured list format. Model running & calibration functions will be added soon.

The output.yaml file should specify:

• Paths to required input files (e.g., bathymetry, metric dictionary, NetCDF model outputs)
• A list of metrics to compute

The core function of the package is cal_metrics(). It reads the YAML configuration file, extracts relevant data, harmonizes variable formats and units, and applies metric functions to generate outputs.

---

cal_metrics(): Main Metric Calculation Function

What it does:

• Loads model output and bathymetry files based on a YAML config
• Extracts variables across different models (GLM, SELMAPROTBAS, WET)
• Applies predefined or custom metric functions
• Returns results as a named list organized by metric and model

---

Input

cal_metrics(
  metric_yaml_file = "output.yaml",   # YAML file defining variables and metrics
  model_filter = "all"                # Options: "GLM", "WET", "SELMAPROTBAS", or "all"
)

---

Output

A nested list:

$MetricName
  $ModelName
    data.frame (datetime × value(s))

Example:

result$Temp_degreeCelcius$GLM
result$Chla_TP_ratio$SELMAPROTBAS

Example Usage

library(LakeEnsemblR.WQ)

result <- cal_metrics("config/output.yaml")

# Plot example: Temperature at 1m depth
plot(result$Temp_degreeCelcius$GLM$datetime,
     result$Temp_degreeCelcius$GLM$Depth_1,
     type = "l", xlab = "Date", ylab = "Temperature (°C) at 1m")

How do I contribute new code back to the LakeEnsemblR.WQ project?

In order to contribute to this code, we recommend the following workflow:

• "fork" this repository to your own personal github account

• clone the github repository to your computer:

• $git clone <git@github.com:{username}/LakeEnsemblR.WQ.git>

• modify code or add new functionality, save the code

add the repository main to a remote main called "upstream"

• $cd LakeEnsemblR.WQ

• $git remote add upstream <git@github.com:aemon-j/LakeEnsemblR.WQ.git>

before pushing your changes to your repository, pull in the current version of the aemon-j main:

• $git fetch upstream

• merge these differences with your own "main" version:

• $git merge upstream/main

push your changes to your github repository, in addition to changes made by pulling in the aemon-j main:

• $git push

submit a pull request to aemon-j main using your account at github.com