New site build

rafalopespx · rafalopespx · commit ecc69daadfd4 · 2025-06-25T00:02:48.000+01:00
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -42,6 +42,18 @@ jobs:
           extra-packages: any::pkgdown, local::.
           needs: website
 
+      - name: Install packages for badge generation
+        run: install.packages(c("badger", "rmarkdown"))
+        shell: Rscript {0}
+
+      - name: Render README
+        run: rmarkdown::render("README.Rmd")
+        shell: Rscript {0}
+        
+      - name: Render index
+        run: rmarkdown::render("index.Rmd")
+        shell: Rscript {0}
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
diff --git a/BADGES.md b/BADGES.md
@@ -0,0 +1,82 @@
+# Badge System Documentation
+
+This document explains how the badge system works for the nowcaster package and how to maintain it.
+
+## Overview
+
+The nowcaster package uses badges to display:
+- Package version (automatically pulled from DESCRIPTION)
+- License information 
+- Lifecycle stage (experimental)
+- R-CMD-check status from GitHub Actions
+
+## Badge Generation
+
+Badges are generated using the `badger` R package in two R Markdown files:
+- `README.Rmd` - generates badges for the GitHub repository README
+- `index.Rmd` - generates badges for the pkgdown website
+
+### Badge Types
+
+1. **Version Badge**: `badger::badge_devel(color = "blue")`
+   - Automatically reads version from DESCRIPTION file
+   - Links to the GitHub repository
+
+2. **License Badge**: `badger::badge_license(url = "https://github.com/covid19br/nowcaster/blob/main/LICENSE.md")`
+   - Shows license type from DESCRIPTION
+   - Links to LICENSE.md file
+
+3. **Lifecycle Badge**: `badger::badge_lifecycle(stage = "experimental")`
+   - Shows development stage
+   - Links to r-lib lifecycle documentation
+
+4. **R-CMD-check Badge**: Static GitHub Actions badge
+   - Shows status of automated R package checks
+   - Updates automatically when checks run
+
+## Build Process
+
+### GitHub Actions (Automated)
+
+The `.github/workflows/pkgdown.yaml` workflow:
+1. Installs necessary R packages (`badger`, `rmarkdown`)
+2. Renders `README.Rmd` to update badges with current package info
+3. Renders `index.Rmd` to update badges for the website
+4. Builds the pkgdown site with updated badges
+5. Deploys to GitHub Pages
+
+### Local Testing
+
+Run the `update_badges.sh` script to test badge generation locally:
+
+```bash
+./update_badges.sh
+```
+
+## Troubleshooting
+
+### Badge not updating
+- Ensure DESCRIPTION file has correct GitHub URL in the URL field
+- Verify `badger` package is installed in build environment
+- Check that R Markdown files are being rendered before site build
+
+### Version showing as hardcoded
+- Remove any `pkg = "package_name"` parameters from `badge_devel()` calls
+- Ensure GitHub repository URL is in DESCRIPTION URL field
+
+### Missing badges on website
+- Verify `index.Rmd` contains all desired badge calls
+- Check that pkgdown workflow includes R Markdown rendering steps
+- Ensure `_pkgdown.yml` includes badges in strips configuration
+
+## Maintenance
+
+When updating package version:
+1. Update version in DESCRIPTION file
+2. Badges will automatically update on next website build
+3. No manual changes needed to badge code
+
+When adding new badges:
+1. Add badge generation code to both `README.Rmd` and `index.Rmd`
+2. Test locally with `update_badges.sh`
+3. Commit changes - badges will update automatically on build
diff --git a/README.Rmd b/README.Rmd
@@ -14,7 +14,7 @@ library(badger)
 <!-- badges: start -->
 <!-- `r badger::badge_cran_checks(pkg = NULL)` -->
 <!-- `r badger::badge_dependencies(pkg = NULL)` -->
-`r badger::badge_devel(pkg = "nowcaster", color = "blue")`
+`r badger::badge_devel(color = "blue")`
 `r badger::badge_license(url = "https://github.com/covid19br/nowcaster/blob/main/LICENSE.md")`
 `r badger::badge_lifecycle(stage = "experimental")`
 [![R-CMD-check](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml)
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 <!-- [![Dependencies](https://tinyverse.netlify.com/badge/nowcaster)](https://cran.r-project.org/package=nowcaster) -->
 
-[![](https://img.shields.io/badge/devel%20version-0.2.3-blue.svg)](https://github.com/nowcaster)
+[![](https://img.shields.io/badge/devel%20version-0.2.3-blue.svg)](https://github.com/covid19br/nowcaster)
 [![License: GPL (\>=
 3)](https://img.shields.io/badge/license-GPL%20(%3E=%203)-blue.svg)](https://github.com/covid19br/nowcaster/blob/main/LICENSE.md)
 [![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -34,4 +34,6 @@ home:
     - citation
     - authors
     - dev
+  strips:
+  - badges
 
diff --git a/index.Rmd b/index.Rmd
@@ -18,9 +18,10 @@ library(badger)
 <!-- badges: start -->
 <!-- `r badger::badge_cran_checks(pkg = NULL)` -->
 <!-- `r badger::badge_dependencies(pkg = NULL)` -->
-`r badger::badge_devel(pkg = "nowcaster", color = "blue")`
+`r badger::badge_devel(color = "blue")`
 `r badger::badge_license(url = "https://github.com/covid19br/nowcaster/blob/main/LICENSE.md")`
 `r badger::badge_lifecycle(stage = "experimental")`
+[![R-CMD-check](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 `nowcaster` is an R package for “nowcasting” epidemiological time-series on individual level data.
diff --git a/update_badges.sh b/update_badges.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# Script to update badges in README and index files
+# This script regenerates the R markdown files to update badges with current package information
+
+echo "Installing required R packages..."
+R --vanilla -e "
+if (!require('badger', quietly = TRUE)) install.packages('badger')
+if (!require('rmarkdown', quietly = TRUE)) install.packages('rmarkdown')
+"
+
+echo "Generating badges to verify they work..."
+R --vanilla -e "
+library(badger)
+cat('Current version badge:', badge_devel(color = 'blue'), '\n')
+cat('License badge:', badge_license(url = 'https://github.com/covid19br/nowcaster/blob/main/LICENSE.md'), '\n')
+cat('Lifecycle badge:', badge_lifecycle(stage = 'experimental'), '\n')
+"
+
+echo "Rendering R markdown files..."
+R --vanilla -e "
+if (requireNamespace('rmarkdown', quietly = TRUE)) {
+  rmarkdown::render('README.Rmd')
+  rmarkdown::render('index.Rmd')
+  cat('Successfully rendered README.Rmd and index.Rmd\n')
+} else {
+  cat('rmarkdown not available - this will be handled by GitHub Actions\n')
+}
+"
+
+echo "Badge update process completed!"
diff --git a/vignettes/articles/1_structured_data.Rmd b/vignettes/articles/1_structured_data.Rmd
@@ -42,10 +42,11 @@ This is the whole premise of nowcasting, we model the case counts at time $t$ gi
 Hence, the model is given by the following:
 
 $$\begin{equation}
-Y_{t,d} \sim NegBinom(\lambda_{t,d}, \phi), \\
-\log(\lambda_{t,d}) = \alpha + \beta_t + \gamma_d, \\
+Y_{t,d} \sim NegBinom(\lambda_{t,d}, \phi) \\
+\log(\lambda_{t,d}) = \alpha + \beta_t + \gamma_d \\
 \beta_t := u_t - u_{(t-1)} - u_{(t-2)} \sim N(0,\tau_{\beta}); \gamma_d := u_d - u_{(d-1)} \sim N(0, \tau_{\gamma})\\
-t=1,2,\ldots,T, \\ d=1,2,\ldots,D,
+t=1,2,\ldots,T \\ 
+d=1,2,\ldots,D \\
 \end{equation}$$
 
 Where the intercept $\alpha$ follows a Gaussian distribution with a very large variance, $\beta_t$ follows a second order random walk with precision $\tau_\beta$, while $\gamma_d$ a first-order random walk with precision $\tau_\gamma$. The model is then completed by INLA default prior distributions for $\phi$, $\tau_\beta$, and $\tau_\gamma$. See [`nbinomial`](https://inla.r-inla-download.org/r-inla.org/doc/likelihood/likelihood-example.pdf), [`rw1`](https://inla.r-inla-download.org/r-inla.org/doc/latent/rw1.pdf) and [`rw2`](https://inla.r-inla-download.org/r-inla.org/doc/latent/rw1.pdf) INLA help pages.
@@ -124,7 +125,10 @@ The first improvement we have done on the baseline model for nowcasting with a n
 $$\begin{equation}Y_{t,d,a} \sim  NegBinom(\lambda_{t,d,a}, \phi), \\
 \log(\lambda_{t,d,a}) =  \alpha_a + \beta_{t,a} + \gamma_{d,a}, \\ 
 \beta_{t,a} := u_t - u_{(t-1)} - u_{(t-2)} \sim N(0,\tau_{a, \beta}); \gamma_{d,a} := u_d - u_{(d-1)} \sim N(0, \tau_{a, \gamma}) \\
-t=1,2,\ldots,T, \\ d=1,2,\ldots,D, \\ a=1,2,\ldots,A, \end{equation}$$
+t=1,2,\ldots,T, \\ 
+d=1,2,\ldots,D, \\ 
+a=1,2,\ldots,A, \\
+\end{equation}$$
 
 where each age class, $a$, has an intercept $\alpha_a$ following a Gaussian distribution with a very large variance, the time-age random effects, $\beta_{t,a}$, follow a joint multivariate Gaussian distribution with a separable variance components an independent Gaussian term for the age classes with precision $\tau_{a,\beta}$ and a second order random walk term for the time with precision $\tau_{\beta}$. Analogously, the delay-age random effects, $\gamma_{d,a}$, follow a joint multivariate Gaussian distribution with a separable variance components an independent Gaussian term for the age classes with precision $\tau_{a,\gamma}$ and a first order random walk term for the time with precision $\tau_{\gamma}$. The model is then completed by INLA default prior distributions for $\phi$, $\tau_{a,\beta}$, $\tau_{a,\gamma}$, $\tau_{a,\beta}$ and $\tau_\gamma$. See [`nbinomial`](https://inla.r-inla-download.org/r-inla.org/doc/likelihood/likelihood-example.pdf), [`rw1`](https://inla.r-inla-download.org/r-inla.org/doc/latent/rw1.pdf) and [`rw2`](https://inla.r-inla-download.org/r-inla.org/doc/latent/rw1.pdf) INLA help pages.
 

-Original file line number
+Diff line change
     - citation
     - authors
     - dev
 +  strips:
 +  - badges