pkgdown website edits + README

Author: CyGei

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -52,3 +52,5 @@ docs
 inst/doc
 /doc/
 /Meta/
+
+/.quarto/

README.Rmd

@@ -6,18 +6,31 @@ output: github_document
 knitr::opts_chunk$set(echo = TRUE)
 ```
 
-# o2ools <a href="https://cygei.github.io/o2ools/"><img src="man/figures/logo.png" align="right" height="138" alt="o2ools website" /></a>
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/CyGei/o2ools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CyGei/o2ools/actions/workflows/R-CMD-check.yaml)
+[![CodeFactor](https://www.codefactor.io/repository/github/cygei/o2ools/badge)](https://www.codefactor.io/repository/github/cygei/o2ools)
+<!-- badges: end -->
 
-Tools to process the results of [outbreaker2](https://github.com/reconhub/outbreaker2).
+# o2ools <a href="https://cygei.github.io/o2ools/"><img src="man/figures/logo.png" alt="o2ools website" align="right" height="242"/></a>
+
+Tools to process the results of [`outbreaker2`](https://github.com/reconhub/outbreaker2).
 
 ## Installation
 
+Install the package from [CRAN](https://cran.r-project.org/web/packages/o2ools/index.html):
+
 ```{r, eval=FALSE}
-# install.packages("devtools")
-devtools::install_github("CyGei/o2ools")
+install.packages("o2ools")
 library(o2ools)
 ```
 
-## Documentation
+Or the development version from GitHub:
+
+```{r, eval=FALSE}
+devtools::install_github("cygei/o2ools")
+```
+
+## Information
 
-For more information, check the vignettes on its dedicated website: [o2ools](https://cygei.github.io/o2ools/)
+The inference of transmission chains from genomic, epidemiological and contact data is central to outbreak investigations. [`outbreaker2`](https://github.com/reconhub/outbreaker2) and other popular models use Bayesian inference to reconstruct who infected whom. However, the results of these models are difficult to interpret and visualise.
+`o2ools` provides tools to analyse and visualise the results of `outbreaker2`. To get started, check the package [vignette](https://cygei.github.io/o2ools/articles/o2ools.html). 

README.md

@@ -1,18 +1,38 @@
 
-# o2ools <a href="https://cygei.github.io/o2ools/"><img src="man/figures/logo.png" align="right" height="138" alt="o2ools website" /></a>
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/CyGei/o2ools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CyGei/o2ools/actions/workflows/R-CMD-check.yaml)
+[![CodeFactor](https://www.codefactor.io/repository/github/cygei/o2ools/badge)](https://www.codefactor.io/repository/github/cygei/o2ools)
+<!-- badges: end -->
+
+# o2ools <a href="https://cygei.github.io/o2ools/"><img src="man/figures/logo.png" alt="o2ools website" align="right" height="242"/></a>
 
 Tools to process the results of
-[outbreaker2](https://github.com/reconhub/outbreaker2).
+[`outbreaker2`](https://github.com/reconhub/outbreaker2).
 
 ## Installation
 
+Install the package from
+[CRAN](https://cran.r-project.org/web/packages/o2ools/index.html):
+
 ``` r
-# install.packages("devtools")
-devtools::install_github("CyGei/o2ools")
+install.packages("o2ools")
 library(o2ools)
 ```
 
-## Documentation
+Or the development version from GitHub:
+
+``` r
+devtools::install_github("cygei/o2ools")
+```
+
+## Information
 
-For more information, check the vignettes on its dedicated website:
-[o2ools](https://cygei.github.io/o2ools/)
+The inference of transmission chains from genomic, epidemiological and
+contact data is central to outbreak investigations.
+[`outbreaker2`](https://github.com/reconhub/outbreaker2) and other
+popular models use Bayesian inference to reconstruct who infected whom.
+However, the results of these models are difficult to interpret and
+visualise. `o2ools` provides tools to analyse and visualise the results
+of `outbreaker2`. To get started, check the package
+[vignette](https://cygei.github.io/o2ools/articles/o2ools.html).

_pkgdown.yml

@@ -1,4 +1,11 @@
 url: https://cygei.github.io/o2ools/
 template:
   bootstrap: 5
-
+  bslib:
+    bootswatch: lux
+    pkgdown-nav-height: 100px
+repo:
+  url:
+    home: https://github.com/CyGei/o2ools
+    issue: https://github.com/CyGei/o2ools/issues
+    user: https://github.com/CyGei