EezyPeezyISIOxy

This repository is being used to develop a workflow for analyzing the ISIMIP-3a data to study the effects of climate change on lake hypolimnetic oxygen dynamics and originated at the GLEON 2022 conference at Lake George, NY.

Contacts: co-champions Carolina Barbosa and Philipp Keller

Working group members: Cayelan Carey, Chloe Faehndrich, Robert Ladwig, Sofia LaFuente, Rafa Marce, Daniel Mercado-Battin, Lipa Nwala

GIT-HUB sources: https://www.youtube.com/watch?v=B-FHx4l1BNU

Instructions

The workflow is implemented using the targets package. The file _targets.R contains the workflow and sets some configuration options. To run it you have to install the following packages:

install.packages(
  c(
    "targets", 
    "tarchetypes", 
    "here", 
    "tibble", 
    "ncdf4", 
    "readr", 
    "dplyr", 
    "rLakeAnalyzer", 
    "pracma", 
    "LakeMetabolizer", 
    "deSolve",
    "tidyr",
    "lubridate",
    "ggplot2",
    "stringr",
    "here",
    "qs"
  )
)

You can run the workflow using targets::tar_make().

For parallel processing you need to install the clustermq package according to the instructions.

To run the script in parallel on your local machine use targets::tar_make_clustermq(workers = 5). Make sure you set the option for clustermq.scheduler to 'multicore' or 'multiprocess'.

Flowchart

graph TD
    A[1 Folder per Lake - Lake 1:n] --> B(output_temp.txt)
    A --> C(output_z.txt)
    A --> D(hypsograph.dat)
    subgraph ide1 [" "]
    B & C & D
    end
    B --> E{Thermal script}
    C --> E
    D --> E
    E --> F(thermal_info.csv)
    F --> G{Oxygen script}
    G --> H(oxygen_info.csv)
    F --to be decided--> I(output.nc)
    H --to be decided--> I