Pre-release epidemics v0.4.0

.github/workflows/dependency-change.yaml

@@ -52,6 +52,12 @@ jobs:
 
  message("Dependencies have changed! Analyzing...")
 
+ if (nrow(deps_added) > 0) {
+ nudge <- "Reach out on slack (`#code-review` or `#help` channels) to double check if there are base R alternatives to the new dependencies.\n"
+ } else {
+ nudge <- ""
+ }
+
  msg <- glue::glue(
  .sep = "\n",
  "This pull request:",
@@ -60,7 +66,8 @@ jobs:
  "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
  "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
  "",
- "(Note that results may be inacurrate if you branched from an outdated version of the target branch.)"
+ nudge,
+ "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"
  )
 
  message("Posting results as a pull request comment.")

.github/workflows/lint-changed-files.yaml

@@ -34,6 +34,7 @@ jobs:
  any::gh
  any::lintr
  any::purrr
+ any::cyclocomp
  epiverse-trace/etdev
  needs: check
 

.github/workflows/pkgdown.yaml

@@ -78,7 +78,7 @@ jobs:
 
  - name: Deploy to GitHub pages 🚀
  if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
- uses: JamesIves/github-pages-deploy-action@v4.5.0
+ uses: JamesIves/github-pages-deploy-action@v4.6.1
  with:
  # We clean on releases because we want to remove old vignettes,
  # figures, etc. that have been deleted from the `main` branch.

.github/workflows/update-copyright-year.yml

@@ -0,0 +1,37 @@
+name: Update copyright year(s) in license file
+
+on:
+ workflow_dispatch:
+ schedule:
+ - cron: '0 3 1 1 *'
+
+permissions:
+ contents: write
+ pull-requests: write
+
+jobs:
+ run:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ fetch-depth: 0
+ - uses: FantasticFiasco/action-update-license-year@v3
+ with:
+ token: ${{ secrets.GITHUB_TOKEN }}
+ path: | 
+ LICENSE.md
+ prBody: >
+ This PR updates the copyright license for this new year! If you're reading this while you're celebrating, enjoy! Don't worry about this one :blush:
+
+ ![Happy new year!](https://media.giphy.com/media/HyDfNCZlTn5iU/giphy.gif?cid=ecf05e4777yl7dbo1xfha6bx1z5lrl13uq7biv6rs9dqsyoh&ep=v1_gifs_search&rid=giphy.gif&ct=g)
+ - uses: FantasticFiasco/action-update-license-year@v3
+ with:
+ token: ${{ secrets.GITHUB_TOKEN }}
+ path: | 
+ LICENSE
+ prBody: >
+ This PR updates the copyright license for this new year! If you're reading this while you're celebrating, enjoy! Don't worry about this one :blush:
+
+ ![Happy new year!](https://media.giphy.com/media/HyDfNCZlTn5iU/giphy.gif?cid=ecf05e4777yl7dbo1xfha6bx1z5lrl13uq7biv6rs9dqsyoh&ep=v1_gifs_search&rid=giphy.gif&ct=g)
+ transform: (?<=YEAR:\s)(?<from>\d{4})?-?(\d{4})?

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: epidemics
 Title: Composable Epidemic Scenario Modelling
-Version: 0.3.0.9000
+Version: 0.4.0
 Authors@R: c(
- person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = c("aut", "cre", "cph"),
+ person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = c("aut", "cph"),
  comment = c(ORCID = "0000-0001-5294-7819")),
- person("Rosalind", "Eggo", , "rosalind.eggo@lshtm.ac.uk", role = c("aut", "cph"),
+ person("Rosalind", "Eggo", , "rosalind.eggo@lshtm.ac.uk", role = c("aut", "cph", "cre"),
  comment = c(ORCID = "0000-0002-0362-6717")),
  person("Edwin", "Van Leeuwen", , "edwin.vanleeuwen@ukhsa.gov.uk", role = c("aut", "cph"),
  comment = c(ORCID = "0000-0002-2383-5305")),
@@ -18,7 +18,9 @@ Authors@R: c(
  person("Joshua W.", "Lambert", , "joshua.lambert@lshtm.ac.uk", role = "rev",
  comment = c(ORCID = "0000-0001-5218-3046")),
  person("James M.", "Azam", , "james.azam@lshtm.ac.uk", role = "rev",
- comment = c(ORCID = "0000-0001-5782-7330"))
+ comment = c(ORCID = "0000-0001-5782-7330")),
+ person("Alexis", "Robert", , "alexis.robert@lshtm.ac.uk", role = "rev",
+ comment = c(ORCID = "0000-0002-4516-2965"))
  )
 Description: A library of compartmental epidemic models taken from the
  published literature, and classes to represent affected populations,

NEWS.md

@@ -1,9 +1,41 @@
-# epidemics (development version)
+# epidemics 0.4.0
+
+Maintainer is changing to @rozeggo.
+
+## Model functions
+
+1. Internal model functions for the models which allow vaccination have been corrected to prevent vaccination introducing negative values of susceptibles; tests added to check for this (#235, initially reported by @avallecam).
+
+## Helper functions
+
+1. Added the `epidemic_peak()` function to calculate the timing and size of the largest peak in each compartment in an scenario model (#240) by @bahadzie.
+
+2. Added the `outcomes_averted()` function to compare epidemic scenarios (e.g. with and without interventions or vaccination) (#225, #230).
 
 ## Documentation
 
 1. Adds a developer-focused vignette on how to modify epidemics and model structures to address potential modelling requests or tasks (#210).
 
+2. Splits up the 'Modelling uncertainty and scenarios' vignette into separate vignettes on uncertainty and scenario comparisons (#225).
+
+3. Removed unnecessary plots from the vignette on modelling vaccination (#235).
+
+4. Fixed link to _socialmixr_ package in the 'Get started' and 'Modelling interventions' vignettes.
+
+5. Updated and added documentation for all new or modified functions.
+
+6. Updated references JSON file.
+
+## Package
+
+1. Updated Codecov GitHub Actions workflow to restore code coverage reporting.
+
+2. Updated package title and citation file. 
+
+3. Updated `_pkgdown.yaml` with new vignette and updated section titles.
+
+4. Updated WORDLIST.
+
 # epidemics 0.3.0
 
 This is a minor version release of _epidemics_ is the end point of this project that allows [vector inputs to the Ebola model](https://github.com/orgs/epiverse-trace/projects/36) (#211, #212).

README.Rmd

@@ -42,6 +42,12 @@ if(!require("pak")) install.packages("pak")
 pak::pkg_install("{{ gh_repo }}")
 ```
 
+Alternatively, install pre-compiled binaries from [the Epiverse TRACE R-universe](https://epiverse-trace.r-universe.dev/epidemics)
+
+```r
+install.packages("epidemics", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
+```
+
 ### Installation Notes
 
 1. Some users who are also using or developing packages that use Stan might face issues if they have modified their toolchain to accommodate packages such as [_cmdstanr_](https://mc-stan.org/cmdstanr/); see [this resolved issue](https://github.com/stan-dev/cmdstanr/issues/790) for a starting point if you face similar problems.

README.md

@@ -48,6 +48,13 @@ if(!require("pak")) install.packages("pak")
 pak::pkg_install("epiverse-trace/epidemics")
 ```
 
+Alternatively, install pre-compiled binaries from [the Epiverse TRACE
+R-universe](https://epiverse-trace.r-universe.dev/epidemics)
+
+``` r
+install.packages("epidemics", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
+```
+
 ### Installation Notes
 
 1. Some users who are also using or developing packages that use Stan