The goal of CSIEM-manual is to provide an easily editable "living manual" that describes the set-up and results of the The Cockburn Sound Integrated Ecosystem Model (CSIEM). The repository is a sub-module within the CSIEM repository available here.

This manual was built using the R bookdown package - an extension of the rmarkdown package designed for writing long-form documents and generating outputs in multiple formats.

Below are basic instructions to help you get started editing the manual. For a detailed contribution guide, please read the Contributing chapter of the manual.

For the best experience, we recommend editing the manual using the RStudio IDE. Once installed, use the console to download the bookdown package:

install.packages("bookdown")

Clone CDM-manualcsiem-science` using GitHub Desktop or from your terminal:

git clone https://github.com/AquaticEcoDynamics/csiem-science.git

Open the R project file CSIEM-manual.Rproj and navigate to the .Rmd file that corresponds with the desired chapter you wish to edit. Once edits have been made, click the 'Build Book' button in RStudio's 'Build' tab to recompile (alternatively use the shortcut Shift + CTRL + B or Shift + ⌘ + B).

Open the R project file CSIEM-manual.Rproj and create a new blank .Rmd file. Write it's contents and save the file as the chapter name written in 'snake case' (e.g. 'Lagoon Water Quality' becomes lagoon_water_quality.Rmd). Navigate to _bookdown.yml and add the chapter .Rmd file to the rmd_files list. Save and re-build the book.

Using GitHub Desktop or your terminal, push the changes back to the csiem_science repository. Updates to the main branch will automatically trigger a re-build of the website (via Github Actions).