From 1f8a65171556c76adfff94af42aede698645966d Mon Sep 17 00:00:00 2001 From: sangeetabhatia03 Date: Sun, 12 Jul 2026 07:22:13 +0100 Subject: [PATCH 1/3] Switch to Bootstrap 5 --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index c5faafed..ee9196ca 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,6 +1,6 @@ url: https://mrc-ide.github.io/EpiEstim template: - bootstrap: 3 + bootstrap: 5 reference: - title: Pre-processing From 6d8718824fca483404ab06e79367f8300cdee4ec Mon Sep 17 00:00:00 2001 From: sangeetabhatia03 Date: Sun, 12 Jul 2026 07:38:41 +0100 Subject: [PATCH 2/3] Update vignette titles in YAML metadata --- vignettes/MV_EpiEstim_vignette.Rmd | 2 +- vignettes/full_EpiEstim_vignette.Rmd | 2 +- vignettes/short_demo.Rmd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/vignettes/MV_EpiEstim_vignette.Rmd b/vignettes/MV_EpiEstim_vignette.Rmd index d416bd0a..6bcbc9b7 100644 --- a/vignettes/MV_EpiEstim_vignette.Rmd +++ b/vignettes/MV_EpiEstim_vignette.Rmd @@ -1,5 +1,5 @@ --- -title: "MV-EpiEstim" +title: "Multivariant EpiEstim" date: "`r Sys.Date()`" output: rmarkdown::html_vignette vignette: > diff --git a/vignettes/full_EpiEstim_vignette.Rmd b/vignettes/full_EpiEstim_vignette.Rmd index 2883d126..f00c97ba 100644 --- a/vignettes/full_EpiEstim_vignette.Rmd +++ b/vignettes/full_EpiEstim_vignette.Rmd @@ -1,5 +1,5 @@ --- -title: "EpiEstim Vignette" +title: "Full EpiEstim vignette" author: "Rebecca Nash" date: "`r Sys.Date()`" output: rmarkdown::html_vignette diff --git a/vignettes/short_demo.Rmd b/vignettes/short_demo.Rmd index 94b05236..57710412 100644 --- a/vignettes/short_demo.Rmd +++ b/vignettes/short_demo.Rmd @@ -1,5 +1,5 @@ --- -title: "EpiEstim: a demonstration" +title: "EpiEstim demonstration" author: "Anne Cori" date: "`r Sys.Date()`" output: rmarkdown::html_vignette From 9fd092fd9730349e3fcf37ab4cb4babd5b9840d2 Mon Sep 17 00:00:00 2001 From: sangeetabhatia03 Date: Sun, 12 Jul 2026 07:39:37 +0100 Subject: [PATCH 3/3] Website URL is expected by pkgdown in DESCRIPTIOM --- DESCRIPTION | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a6368f98..510f749f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -25,7 +25,8 @@ Description: Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) and Wallinga and Teunis (2004) . -URL: https://github.com/mrc-ide/EpiEstim +URL: https://mrc-ide.github.io/EpiEstim, + https://github.com/mrc-ide/EpiEstim BugReports: https://github.com/mrc-ide/EpiEstim/issues Depends: R (>= 3.3.0) Imports: @@ -58,6 +59,6 @@ License: GPL (>=2) LazyLoad: yes Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 VignetteBuilder: knitr Remotes: reconverse/incidence2/pkg +Config/roxygen2/version: 8.0.0