diff --git a/README.md b/README.md index 81c1caa..d8e0246 100644 --- a/README.md +++ b/README.md @@ -1,59 +1,21 @@ -# Containerised R workflow template +# WABNet-spatial -[![Project Status: WIP – Initial development is in progress, but there -has not yet been a stable, usable release suitable for the -public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) +[![Project Status: Active – The project has reached a stable, usable +state and is being actively +developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#wip) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![container-workflow-template](https://github.com/ecohealthalliance/container-template/actions/workflows/container-workflow-template.yml/badge.svg)](https://github.com/ecohealthalliance/container-template/actions/workflows/container-workflow-template.yml) -This is a template repository of a containerised R workflow built on the -`targets` framework, made portable using `renv`, and ran manually or -automatically using `GitHub Actions`. To use this template click on the -“use this template button” and then select create a new repository. - -Check out the -[`containerTemplateUtils`](https://github.com/ecohealthalliance/containerTemplateUtils) -package for handling common tasks related to this repo (sending emails, -uploading files to AWS, etc. ) - -Note that `git-crypt` is not part of the template repo. See the [EHA M&A -handbook](https://ecohealthalliance.github.io/eha-ma-handbook/16-encryption.html#set-up-encryption-for-a-repo-that-did-not-previously-use-git-crypt) -for how to add git-crypt. - -Follow the links for more information about: - -- [`targets`](https://ecohealthalliance.github.io/eha-ma-handbook/3-projects.html#targets) -- [`renv`](https://ecohealthalliance.github.io/eha-ma-handbook/3-projects.html#package-management-with-renv) -- [git-crypt](https://ecohealthalliance.github.io/eha-ma-handbook/16-encryption.html) -- [Reproducible - workflows](https://github.com/ecohealthalliance/building-blocks-of-reproducibility) - -Recommendations: -- One function per file in R/ -- Non-function R scripts in another directory like `scripts/` -- Use the same names for targets and function arguments for those -targets unless a function -- Nouns for targets, verbs for functions -- Use common suffixes for target types: `_file` for files, `_raw` for -read-in but unprocessed data -- Use `fnmate` and `tflow` RStudio Add-Ins to make this easy, create -shortcuts for these add-ins -([talk](https://www.youtube.com/watch?v=jU1Zv21GvT4)), or the `usethis` -package - -## Quick start - -- Create repo from template -- rename .Rproj file -- streamline packages in `packages.R` -- modify `.gitattributes` to include any files that may need encryption -- initialize `git-crypt` for repo -- add relevant environment variables to `.env` file -- rename github actions workflows +This repository contains code to produce figures in the Final Technical +Report for the project, “Understanding the Risk of Bat-Borne Zoonotic +Disease Emergence in Western Asia” (HDTRA1-17-1-0064). This project +identified key factors correlated with the risk of bat viral zoonoses +from sites across Western Asia. The data needed to reproduce the +analyses are in the process of being uploaded to separate repositories. +Contact with questions.