diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..b423ff3
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,27 @@
+^LICENSE\.md$
+^\.devcontainer$
+^data-raw$
+^README\.Rmd$
+^\.github$
+^\.pre-commit-config\.yaml$
+^\.lintr$
+^\.Rprofile
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^vignettes/cache$
+^.*\.Rproj$
+^\.Rproj\.user$
+^codemeta\.json$
+^inst/make_hexsticker\.R$
+^inst/scripts$
+^vignettes/precompile\.R$
+^vignettes/chunks$
+^doc$
+^Meta$
+^\.vscode$
+^CITATION\.cff$
+^vignettes/using-stan-tools\.Rmd$
+^touchstone$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..991bda2
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,57 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+ push:
+ branches:
+ - main
+ schedule:
+ - cron: '5 4 * * 1'
+ pull_request:
+ branches:
+ - main
+ merge_group:
+ workflow_dispatch:
+
+name: R-CMD-check
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.head_ref }}
+ cancel-in-progress: true
+
+jobs:
+ R-CMD-check:
+ if: "! contains(github.event.head_commit.message, '[ci skip]')"
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'oldrel-1'}
+ - {os: macOS-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+ NOT_CRAN: true
+
+ 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 }}
+ 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
diff --git a/.github/workflows/codemeta.yaml b/.github/workflows/codemeta.yaml
new file mode 100644
index 0000000..b7e17da
--- /dev/null
+++ b/.github/workflows/codemeta.yaml
@@ -0,0 +1,44 @@
+on:
+ push:
+ paths:
+ - DESCRIPTION
+ - .github/workflows/codemeta.yml
+ workflow_dispatch:
+
+name: Render codemeta
+
+jobs:
+ render:
+ runs-on: ubuntu-latest
+ if: "!contains(github.event.head_commit.message, 'cm-skip')"
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::codemetar
+ needs: codemeta
+
+ - name: Render codemeta
+ run: codemetar::write_codemeta()
+ shell: Rscript {0}
+
+ - name: Create Pull Request
+ if: github.ref == 'refs/heads/main'
+ uses: peter-evans/create-pull-request@v7
+ with:
+ commit-message: "Update codemeta.json"
+ title: "Update codemeta.json"
+ body: "This is an automated pull request to update the codemeta.json file."
+ branch: "update-codemeta-${{ github.run_number }}"
+ labels: "metadata"
+ reviewers: seabbs
+ add-paths: |
+ codemeta.json
+ token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml
new file mode 100644
index 0000000..61d45bd
--- /dev/null
+++ b/.github/workflows/lint-changed-files.yaml
@@ -0,0 +1,49 @@
+# 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:
+ pull_request:
+ branches:
+ - main
+ workflow_dispatch:
+
+name: lint-changed-files
+
+jobs:
+ lint-changed-files:
+ runs-on: ubuntu-latest
+ if: "! contains(github.event.head_commit.message, '[ci skip]')"
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: |
+ any::gh
+ any::lintr
+ any::purrr
+ needs: check
+
+ - name: Add lintr options
+ run: |
+ cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
+ shell: Rscript {0}
+
+ - name: Install package
+ run: R CMD INSTALL .
+
+ - name: Extract and lint files changed by this PR
+ run: |
+ files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+ changed_files <- purrr::map_chr(files, "filename")
+ all_files <- list.files(recursive = TRUE)
+ exclusions_list <- as.list(setdiff(all_files, changed_files))
+ lintr::lint_package(exclusions = exclusions_list)
+ shell: Rscript {0}
+ env:
+ LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..b081cd8
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,53 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main]
+ workflow_dispatch:
+ pull_request:
+ branches:
+ - main
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.head_ref }}
+ cancel-in-progress: true
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::pkgdown, local::.
+ needs: website
+
+ - name: Build site
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
+
+ - name: Upload website
+ uses: actions/upload-artifact@v4
+ with:
+ name: website
+ retention-days: 5
+ path: docs
+
+ - name: Deploy to GitHub pages 🚀
+ if: github.event_name != 'pull_request'
+ uses: JamesIves/github-pages-deploy-action@v4.7.2
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
new file mode 100644
index 0000000..f49b721
--- /dev/null
+++ b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,109 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ issue_comment:
+ types: [created]
+
+name: Commands
+
+jobs:
+ document:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/document') }}
+ name: document
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: roxygen2
+
+ - name: Document
+ run: Rscript -e 'roxygen2::roxygenise()'
+
+ - name: commit
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+ git add man/\* NAMESPACE
+ git commit -m 'Document'
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ style:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/style') }}
+ name: style
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+
+ - name: Install dependencies
+ run: Rscript -e 'install.packages(c("styler", "roxygen2"))'
+
+ - name: Style
+ run: Rscript -e 'styler::style_pkg()'
+
+ - name: commit
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+ git add \*.R
+ git commit -m 'Style'
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ update_wordlist:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/update_wordlist') }}
+ name: update_wordlist
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+
+ - name: Install dependencies
+ run: |
+ install.packages(c("spelling"))
+ shell: Rscript {0}
+
+ - name: Update wordlist
+ run: |
+ spelling::update_wordlist(confirm = TRUE)
+ shell: Rscript {0}
+
+ - name: Commit changes
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+ git add inst/WORDLIST
+ git commit -m 'Update wordlist' || echo "No changes to commit"
+
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/render-readme.yaml b/.github/workflows/render-readme.yaml
new file mode 100644
index 0000000..d5b2d22
--- /dev/null
+++ b/.github/workflows/render-readme.yaml
@@ -0,0 +1,64 @@
+name: render-readme
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.head_ref }}
+ cancel-in-progress: true
+
+on:
+ workflow_dispatch:
+ push:
+ branches:
+ - main
+
+jobs:
+ render-readme:
+ runs-on: macos-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - name: Checkout repos
+ uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - name: Setup pandoc
+ uses: r-lib/actions/setup-pandoc@v2
+
+ - name: Install dependencies
+ uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rmarkdown, local::.
+
+ - name: Update contributors
+ if: github.ref == 'refs/heads/main'
+ run: allcontributors::add_contributors(format = "text")
+ shell: Rscript {0}
+
+ - name: Compile the readme
+ run: |
+ rmarkdown::render("README.Rmd")
+ shell: Rscript {0}
+
+ - name: Upload README.md as an artifact
+ uses: actions/upload-artifact@v4
+ with:
+ name: readme
+ path: README.md
+
+ - name: Create Pull Request
+ if: github.ref == 'refs/heads/main'
+ uses: peter-evans/create-pull-request@v7
+ with:
+ commit-message: "Automatic README update"
+ title: "Update README"
+ body: "This is an automated pull request to update the README."
+ branch: "update-readme-${{ github.run_number }}"
+ labels: "documentation"
+ reviewers: kaitejohnson
+ add-paths: |
+ README.Rmd
+ README.md
+ inst/WORDLIST
+ token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..39617d8
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,39 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+ workflow_dispatch:
+ merge_group:
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.head_ref }}
+ cancel-in-progress: true
+
+name: test-coverage
+
+jobs:
+ test-coverage:
+ runs-on: ubuntu-latest
+ if: "! contains(github.event.head_commit.message, '[ci skip]')"
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ NOT_CRAN: true
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::covr
+ needs: coverage
+
+ - name: Test coverage
+ run: covr::codecov(quiet = FALSE, token = "${{ secrets.CODECOV_TOKEN }}")
+ shell: Rscript {0}
diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml
new file mode 100644
index 0000000..905a99e
--- /dev/null
+++ b/.github/workflows/update-citation-cff.yaml
@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+ push:
+ tags-ignore:
+ - '*'
+ paths:
+ - DESCRIPTION
+ - inst/CITATION
+ - .github/workflows/update-citation-cff.yaml
+ workflow_dispatch:
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.head_ref }}
+ cancel-in-progress: true
+
+name: Update CITATION.cff
+
+jobs:
+ update-citation-cff:
+ runs-on: macos-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: |
+ any::cffr
+ any::V8
+ - name: Update CITATION.cff
+ run: |
+ library(cffr)
+ # Customize with your own code
+ # See https://docs.ropensci.org/cffr/articles/cffr.html
+ # Write your own keys
+ mykeys <- list()
+ # Create your CITATION.cff file
+ cff_write(keys = mykeys)
+ shell: Rscript {0}
+
+ - name: Create Pull Request
+ if: github.ref == 'refs/heads/main'
+ uses: peter-evans/create-pull-request@v7
+ with:
+ commit-message: "Update CITATION.cff"
+ title: "Update CITATION.cff"
+ body: "This is an automated pull request to update the CITATION.cff file."
+ branch: "update-citation-cff-${{ github.run_number }}"
+ labels: "documentation"
+ reviewers: seabbs
+ add-paths: |
+ CITATION.cff
+ token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..a3d0602
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,23 @@
+*.xlsx
+output
+*.rds
+inst/doc
+*.tex
+*.log
+_targets
+docs
+cache
+.DS_Store
+.Rproj.user
+*.Rproj
+!inst/extdata/*.rds
+/doc/
+/Meta/
+*.Rhistory
+.vscode
+/figures/
+/vignettes/*_cache/
+.here
+*.pdf
+*.html
+CRAN-SUBMISSION
diff --git a/.lintr b/.lintr
new file mode 100644
index 0000000..fda3d78
--- /dev/null
+++ b/.lintr
@@ -0,0 +1,16 @@
+linters: all_linters(
+ packages = "lintr",
+ implicit_integer_linter = NULL,
+ extraction_operator_linter = NULL,
+ undesirable_function_linter = NULL,
+ function_argument_linter = NULL,
+ indentation_linter = NULL,
+ object_name_linter = NULL,
+ cyclocomp_linter(25L)
+ )
+exclusions: list(
+ "inst",
+ "tests/testthat.R" = list(
+ unused_import_linter = Inf
+ )
+ )
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..4a228d5
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,39 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+- repo: https://github.com/lorenzwalthert/precommit
+ rev: v0.4.3
+ hooks:
+ - id: style-files
+ args: [--style_pkg=styler, --style_fun=tidyverse_style]
+ # codemeta must be above use-tidy-description when both are used
+ # - id: codemeta-description-updated
+ - id: use-tidy-description
+ - id: lintr
+ - id: parsable-R
+ - id: no-browser-statement
+ - id: deps-in-desc
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.6.0
+ hooks:
+ - id: check-added-large-files
+ args: ['--maxkb=200']
+ - id: end-of-file-fixer
+ exclude: '\.Rd'
+- repo: local
+ hooks:
+ - id: forbid-to-commit
+ name: Don't commit common R artifacts
+ entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+ language: fail
+ files: '\.Rhistory|\.RData|\.Rds|\.rds$'
+- repo: meta
+ hooks:
+ - id: check-hooks-apply
+ - id: check-useless-excludes
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.6.0
+ hooks:
+ - id: trailing-whitespace
+ - id: check-yaml
+ - id: check-added-large-files
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..5d12fd7
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,173 @@
+# --------------------------------------------
+# CITATION file created with {cffr} R package
+# See also: https://docs.ropensci.org/cffr/
+# --------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "baselinenowcast" in publications use:'
+type: software
+license: MIT
+title: 'baselinenowcast: Baseline nowcast from right-truncated epidemiological data'
+version: 0.1.0.1000
+doi: 10.5281/zenodo.13632839
+identifiers:
+- type: url
+ value: https://github.com/epinowcast/baselinenowcast/
+abstract: This package provides R functions to implement nowcasting from
+ right-truncated epidemiological case data
+authors:
+- name: Kaitlyn Johnson
+ email: kaitlyn.johnson@lshtm.ac.uk
+ orcid: https://orcid.org/0000-0001-8011-0012
+- name: Sam Abbott
+ email: contact@samabbott.co.uk
+ orcid: https://orcid.org/0000-0001-8057-8037
+- name: Sebastian Funk
+ email: sebastian.funk@lshtm.ac.uk
+ orcid: https://orcid.org/0000-0002-2842-3406
+- name: Johannes Bracher
+ email: johannes.bracher@kit.edu
+ orcid: https://orcid.org/0000-0002-3777-1410
+preferred-citation:
+ type: manual
+ title: 'baselinenowcast: Baseline nowcast from right-truncated epidemiological data'
+ authors:
+ - name: Kaitlyn Johnson
+ email: kaitlyn.johnson@lshtm.ac.uk
+ orcid: https://orcid.org/0000-0001-8011-0012
+ - name: Sam Abbott
+ email: contact@samabbott.co.uk
+ orcid: https://orcid.org/0000-0001-8057-8037
+ - name: Sebastian Funk
+ email: sebastian.funk@lshtm.ac.uk
+ orcid: https://orcid.org/0000-0002-2842-3406
+ - name: Johannes Bracher
+ email: johannes.bracher@kit.edu
+ orcid: https://orcid.org/0000-0002-3777-1410
+ year: '2025'
+repository-code: https://github.com/epinowcast/baselinenowcast/issues/
+url: https://baselinenowcast.epinowcast.org
+contact:
+- name: Kaitlyn Johnson
+ email: kaitlyn.johnson@lshtm.ac.uk
+ orcid: https://orcid.org/0000-0001-8011-0012
+references:
+- type: software
+ title: 'R: A Language and Environment for Statistical Computing'
+ notes: Depends
+ url: https://www.R-project.org/
+ authors:
+ - name: R Core Team
+ institution:
+ name: R Foundation for Statistical Computing
+ address: Vienna, Austria
+ year: '2024'
+ version: '>= 4.0.0'
+- type: software
+ title: bookdown
+ abstract: 'bookdown: Authoring Books and Technical Documents with R Markdown'
+ notes: Suggests
+ url: https://pkgs.rstudio.com/bookdown/
+ repository: https://CRAN.R-project.org/package=bookdown
+ authors:
+ - family-names: Xie
+ given-names: Yihui
+ email: xie@yihui.name
+ orcid: https://orcid.org/0000-0003-0645-5666
+ year: '2024'
+ doi: 10.32614/CRAN.package.bookdown
+- type: software
+ title: knitr
+ abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
+ notes: Suggests
+ url: https://yihui.org/knitr/
+ repository: https://CRAN.R-project.org/package=knitr
+ authors:
+ - family-names: Xie
+ given-names: Yihui
+ email: xie@yihui.name
+ orcid: https://orcid.org/0000-0003-0645-5666
+ year: '2024'
+ doi: 10.32614/CRAN.package.knitr
+- type: software
+ title: rmarkdown
+ abstract: 'rmarkdown: Dynamic Documents for R'
+ notes: Suggests
+ url: https://pkgs.rstudio.com/rmarkdown/
+ repository: https://CRAN.R-project.org/package=rmarkdown
+ authors:
+ - family-names: Allaire
+ given-names: JJ
+ email: jj@posit.co
+ - family-names: Xie
+ given-names: Yihui
+ email: xie@yihui.name
+ orcid: https://orcid.org/0000-0003-0645-5666
+ - family-names: Dervieux
+ given-names: Christophe
+ email: cderv@posit.co
+ orcid: https://orcid.org/0000-0003-4474-2498
+ - family-names: McPherson
+ given-names: Jonathan
+ email: jonathan@posit.co
+ - family-names: Luraschi
+ given-names: Javier
+ - family-names: Ushey
+ given-names: Kevin
+ email: kevin@posit.co
+ - family-names: Atkins
+ given-names: Aron
+ email: aron@posit.co
+ - family-names: Wickham
+ given-names: Hadley
+ email: hadley@posit.co
+ - family-names: Cheng
+ given-names: Joe
+ email: joe@posit.co
+ - family-names: Chang
+ given-names: Winston
+ email: winston@posit.co
+ - family-names: Iannone
+ given-names: Richard
+ email: rich@posit.co
+ orcid: https://orcid.org/0000-0003-3925-190X
+ year: '2024'
+ doi: 10.32614/CRAN.package.rmarkdown
+- type: software
+ title: testthat
+ abstract: 'testthat: Unit Testing for R'
+ notes: Suggests
+ url: https://testthat.r-lib.org
+ repository: https://CRAN.R-project.org/package=testthat
+ authors:
+ - family-names: Wickham
+ given-names: Hadley
+ email: hadley@posit.co
+ year: '2024'
+ doi: 10.32614/CRAN.package.testthat
+ version: '>= 3.1.9'
+- type: software
+ title: usethis
+ abstract: 'usethis: Automate Package and Project Setup'
+ notes: Suggests
+ url: https://usethis.r-lib.org
+ repository: https://CRAN.R-project.org/package=usethis
+ authors:
+ - family-names: Wickham
+ given-names: Hadley
+ email: hadley@posit.co
+ orcid: https://orcid.org/0000-0003-4757-117X
+ - family-names: Bryan
+ given-names: Jennifer
+ email: jenny@posit.co
+ orcid: https://orcid.org/0000-0002-6983-2759
+ - family-names: Barrett
+ given-names: Malcolm
+ email: malcolmbarrett@gmail.com
+ orcid: https://orcid.org/0000-0003-0299-5825
+ - family-names: Teucher
+ given-names: Andy
+ email: andy.teucher@posit.co
+ orcid: https://orcid.org/0000-0002-7840-692X
+ year: '2024'
+ doi: 10.32614/CRAN.package.usethis
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..ec8bd93
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,48 @@
+Package: baselinenowcast
+Title: Baseline nowcast
+Version: 0.0.0.1000
+Authors@R:
+ c(person(given = "Kaitlyn",
+ family = "Johnson",
+ role = c("aut", "cre", "cph"),
+ email = "kaitlyn.johnson@lshtm.ac.uk",
+ comment = c(ORCID = "0000-0001-8011-0012")),
+ person(given = "Sam",
+ family = "Abbott",
+ role = c("aut"),
+ email = "contact@samabbott.co.uk",
+ comment = c(ORCID = "0000-0001-8057-8037")),
+ person(given = "Johannes",
+ family = "Bracher",
+ role = c("aut"),
+ email = "johannes.bracher@kit.edu",
+ comment = c(ORCID = "0000-0002-3777-1410")),
+ person(given = "Sebastian",
+ family = "Funk",
+ role = c("aut"),
+ email = "sebastian.funk@lshtm.ac.uk",
+ comment = c(ORCID = "0000-0002-2842-3406")))
+Description: Provides functions for nowcasting right-truncated epidemiological
+ data, based heavily on the method implemented in
+ https://github.com/KITmetricslab/RESPINOW-Hub/tree/main/code/baseline
+License: MIT + file LICENSE
+URL: https://github.com/epinowcast/baselinenowcast/
+BugReports: https://github.com/epinowcast/baselinenowcast/issues
+Depends:
+ R (>= 4.0.0)
+Suggests:
+ dplyr,
+ bookdown,
+ ggplot2,
+ spelling,
+ rmarkdown,
+ testthat (>= 3.1.9),
+ usethis,
+ withr,
+ knitr
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+VignetteBuilder: knitr
+Config/Needs/hexsticker: hexSticker, sysfonts, ggplot2
+Config/Needs/website: r-lib/pkgdown, epinowcast/enwtheme
diff --git a/LICENSE b/LICENSE
index 52ae40b..b81dba3 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2025 Epinowcast
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2025
+COPYRIGHT HOLDER: baselinenowcast authors
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..1ccc257
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2025 baselinenowcast authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..e651b94
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1 @@
+# Generated by roxygen2: do not edit by hand
diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 0000000..7b180ec
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,3 @@
+# baselinenowcast 0.0.0.1000
+
+- Added package skeleton.
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 0000000..93acb93
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,9 @@
+#' Escape brackets returned in a string for passing to glue
+#'
+#' @param string A string vector containing `{}`
+#'
+#' @return A string vector where all single brackets are replaced with double
+#' brackets
+autoescape_brackets <- function(string) {
+ return(gsub("\\{|\\}", "", string))
+}
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 0000000..2ac0dc2
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,78 @@
+---
+output: github_document
+---
+
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "",
+ fig.path = file.path("man", "figures", "README-"),
+ out.width = "100%",
+ dpi = 330,
+ message = FALSE, warning = FALSE
+)
+```
+# Baseline nowcast
+
+
+[](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[](https://github.com/epinowcast/baselinenowcast/actions/workflows/R-CMD-check.yaml) [](https://app.codecov.io/gh/epinowcast/baselinenowcast)
+
+[](https://epinowcast.r-universe.dev/baselinenowcast)
+[](https://github.com/epinowcast/baselinenowcast/blob/master/LICENSE.md/)
+[](https://github.com/epinowcast/baselinenowcast/graphs/contributors)
+
+
+## Summary
+
+```{r, results = "asis", echo=FALSE}
+cat(gsub("\n[ ]+", " ", packageDescription("baselinenowcast")$Description))
+```
+
+## Installation
+
+Installing the package
+
+```{r, child="vignettes/chunks/_readme-install-baselinenowcast.Rmd"}
+```
+
+Organisation Website
+
+Our [organisation website](https://www.epinowcast.org/) includes links to other resources, [guest posts](https://www.epinowcast.org/blog.html), and [seminar schedule](https://www.epinowcast.org/seminars.html) for both upcoming and past recordings.
+
+Community Forum
+
+Our [community forum](https://community.epinowcast.org/) has areas for [question and answer](https://community.epinowcast.org/c/interface/15) and [considering new methods and tools](https://community.epinowcast.org/c/projects/11), among others. If you are generally interested in real-time analysis of infectious disease, you may find this useful even if you do not use `baselinenowcast`.
+
+