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epiwave.pipelines

https://github.com/idem-lab/epiwave.pipelines

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: idem-lab
  • Language: R
  • Default Branch: main
  • Size: 745 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 3
  • Open Issues: 14
  • Releases: 2
Created almost 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Citation

README.md

epiwave.pipelines

DOI

Repository for the new $Reff$ model using Gaussian Processes with greta. This model is centered on estimation of the infection timeseries, from which $Reff$ 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 ```

  1. 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'

  1. 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)

  2. 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>

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

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

  1. 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.

Owner

  • Name: The Infectious Disease Ecology and Modelling Team
  • Login: idem-lab
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Windecker"
  given-names: "Saras Mei"
  orcid: "https://orcid.org/0000-0002-4870-8353"
- family-names: "Hao"
  given-names: "Tianxiao"
  orcid: "https://orcid.org/0000-0003-4363-1956"
- family-names: "Senior"
  given-names: "Kate"
  orcid: "https://orcid.org/0000-0003-1123-1472"
- family-names: "Golding"
  given-names: "Nick"
  orcid: "https://orcid.org/0000-0001-8916-5570"
title: "idem-lab/epiwave.pipelines: First minor release"
version: v.0.0.9-DEV
date-released: 2023-12-18
<<<<<<< HEAD
doi: XXXXXX
url: "https://github.com/idem-lab/epiwave.pipelines"
=======
doi: 10.5281/zenodo.10400665
url: "https://github.com/idem-lab/GPreff"
>>>>>>> origin/main

GitHub Events

Total
  • Release event: 1
  • Create event: 1
Last Year
  • Release event: 1
  • Create event: 1

Dependencies

DESCRIPTION cran
  • greta.gpgreta.dynamics * imports
  • testthat >= 3.0.0 suggests