epiwave.pipelines

Repository for the new $R_eff$ model using Gaussian Processes with greta. This model is centered on estimation of the infection timeseries, from which $R_eff$ can be calculated when we add generation interval information.

This workflow has separate components for PCR and RAT data, and estimates separately by jurisdiction, in this case Australian state.

Instructions for contributing to this repository

Setting up

1. Fork this repo into personal GitHub account
2. Navigate to your fork [username]/epiwave.pipelines and clone a local version to your machine
3. Open new project from version control in local RStudio

4. Configure your remote repository

   • list remotes

     git remote -v
     > origin  git@github.com:[YOURUSERNAME]/epiwave.pipelines.git (fetch)
     > origin  git@github.com:[YOURUSERNAME]/epiwave.pipelines.git (push)

   • add upstream

     git remote add upstream git@github.com:idem-lab/epiwave.pipelines.git

   • verify by checking remotes again

     git remote -v
     > origin  git@github.com:[YOURUSERNAME]/epiwave.pipelines.git (fetch)
     > origin  git@github.com:[YOURUSERNAME]/epiwave.pipelines.git (push)
     > upstream        git@github.com:idem-lab/epiwave.pipelines.git (fetch)
     > upstream        git@github.com:idem-lab/epiwave.pipelines.git (push)

Making changes

1. Before beginning new work, make sure your fork is up to date with the remote

   # if you are not on main branch
   git checkout main
   
   # fetch from upstream repo
   git fetch upstream main
   
   # then merge
   git merge upstream/main

2. Make a new branch for your changes using:

   git checkout -b ＜dev-branch＞

   Try and use a descriptive name for the new branch, for example 'updateCAR'

3. When you've made your changes, commit all changes to your branch, then repeat step 1 if necessary (if there have been changes to upstream)

4. Merge your new branch into your main, using --no-ff to indicate 'no fast forward' because we want a commit recording the merge

   git checkout main
   git merge --no-ff <dev-branch>

5. Add commit message, then push to origin and delete dev branch

   git push origin main
   git branch --delete <dev-branch>

6. Create pull request on GitHub

Resources

• For more on working with branches, see here.
• For more on forks and working with upstreams, see here.
• For more on merging and rebasing, see here.