From b1a7e2bd2a3d3302c10ea29d5755baf3e2527bfc Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:15:51 +0100 Subject: [PATCH 1/9] remove travis and appveyor --- .travis.yml | 41 ----------------------------------------- appveyor.yml | 45 --------------------------------------------- 2 files changed, 86 deletions(-) delete mode 100644 .travis.yml delete mode 100644 appveyor.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 9ba58d6e..00000000 --- a/.travis.yml +++ /dev/null @@ -1,41 +0,0 @@ -# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r -language: r -cache: packages - -addons: - apt: - sources: - - sourceline: 'ppa:chris-lea/libsodium' - - sourceline: 'ppa:opencpu/jq' - packages: - - libsodium-dev - - libprotobuf-dev - - libprotoc-dev - - protobuf-compiler - - libudunits2-dev - - libv8-3.14-dev - - libjq-dev - - libgdal-dev - -matrix: - include: - - os: linux - r: release - env: - - R_CODECOV=true - - os: linux - r: devel - - os: linux - r: oldrel - - os: osx - osx_image: xcode8.3 - -warnings_are_errors: true - -notifications: - email: - on_success: change - on_failure: change - -after_success: -- if [[ "${R_CODECOV}" ]]; then Rscript -e 'covr::codecov()'; fi diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index e16dcbf5..00000000 --- a/appveyor.yml +++ /dev/null @@ -1,45 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -install: - ps: Bootstrap - -# cache: -# - C:\RLibrary - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits From 81ec9630272aa08669086df992917d4f3fc9ac2c Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:18:05 +0100 Subject: [PATCH 2/9] update description with with orgs --- DESCRIPTION | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index fc924134..994031b7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,7 +31,11 @@ Authors@R: role = "ctb"), person(given = "Neale", family = "Batra", - role = "ctb")) + role = "ctb"), + person("Applied Epi Incorporated", + role = "cph"), + person("Medecins Sans Frontieres Operational Centre Amsterdam", + role = "fnd")) Description: A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages: epitabulate (for epidemiological tables), epidict From 37fb39f7378228da58283e93304c6368fb416c6f Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:32:04 +0100 Subject: [PATCH 3/9] update gh actions --- .github/workflows/R-CMD-check.yaml | 104 +++++++-------------------- .github/workflows/pkgdown.yaml | 66 +++++++++-------- .github/workflows/test-coverage.yaml | 62 ++++++++++++++++ 3 files changed, 121 insertions(+), 111 deletions(-) create mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 76494b47..d46a6175 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,18 +1,14 @@ -# NOTE: This workflow is overkill for most R packages -# check-standard.yaml is likely a better choice -# usethis::use_github_action("check-standard") will install it. -# -# 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 +# 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: - - master + branches: [main, master] pull_request: - branches: - - master + branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -24,85 +20,33 @@ jobs: fail-fast: false matrix: config: - - {os: macOS-latest, cov: 'true', r: 'release'} - - {os: windows-latest,cov: 'false', r: 'release'} - - {os: windows-latest,cov: 'false', r: '3.6'} - - {os: ubuntu-16.04, cov: 'false', r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } - - {os: ubuntu-16.04, cov: 'false', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, cov: 'false', r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, cov: 'false', r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, cov: 'false', r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {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: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@master + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@master - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "16.04"), sep = "\n")') - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Session info - run: | - options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - - name: Show testthat output - if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Cover - if: matrix.config.cov == 'true' - run: covr::codecov() - shell: Rscript {0} + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 8bc92105..4bbce750 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -1,46 +1,50 @@ +# 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: master + branches: [main, master] + pull_request: + branches: [main, master] + release: + types: [published] + workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: - runs-on: macOS-latest + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@master + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-pandoc@master + - uses: r-lib/actions/setup-pandoc@v2 - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - name: Cache R packages - uses: actions/cache@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - install.packages("pkgdown") - shell: Rscript {0} + extra-packages: any::pkgdown, local::. + needs: website - - name: Install package - run: R CMD INSTALL . + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} - - name: Deploy package - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 00000000..0ab748d6 --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,62 @@ +# 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: test-coverage.yaml + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-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::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + print(cov) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v5 + with: + # Fail if error if not on PR, or if on PR and token is given + fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} + files: ./cobertura.xml + plugins: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package From 617a04aa3960ff305aa4dc650ef14e58d5a96b8a Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:32:19 +0100 Subject: [PATCH 4/9] update readme badges --- README.md | 52 ++++++++++++++++++++++++++++------------------------ 1 file changed, 28 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 2c2531d7..655be43f 100644 --- a/README.md +++ b/README.md @@ -6,27 +6,24 @@ [![Lifecycle: -maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) +maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing) [![CRAN status](https://www.r-pkg.org/badges/version/sitrep)](https://CRAN.R-project.org/package=sitrep) +[![R-CMD-check](https://github.com/R4EPI/sitrep/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/R4EPI/sitrep/actions/workflows/R-CMD-check.yaml) [![Codecov test -coverage](https://codecov.io/gh/R4EPI/sitrep/branch/master/graph/badge.svg)](https://codecov.io/gh/R4EPI/sitrep?branch=master) -[![R build -status](https://github.com/R4EPI/sitrep/workflows/R-CMD-check/badge.svg)](https://github.com/R4EPI/sitrep/actions) +coverage](https://codecov.io/gh/R4EPI/sitrep/graph/badge.svg)](https://app.codecov.io/gh/R4EPI/sitrep) The goal of {sitrep} is provide report templates for common epidemiological surveys and outbreak reports. The package further contains helper function that standardize certain analyses. -While templates are primarily for MSF analyses - they have been setup to -be as generic as possible for use by the general applied epidemiology -community. +While templates are primarily for Medecins Sans Frontieres analyses - +they have been setup to be as generic as possible for use by the general +applied epidemiology community. -**Detailed information about the project and the templates can be found -at .** -A reference website for the functions in {sitrep} can be found at -. +**Detailed information about the project, the templates and functions in +{sitrep} can be found at .** {sitrep} includes a number of other *R* packages which facilitate specific analysis: @@ -53,14 +50,9 @@ package. remotes::install_github("r4epi/sitrep") ``` -If you are getting errors, check the [frequently asked -questions](https://r4epis.netlify.com/faq/). - ## Available templates -Sitrep has [four outbreak -templates](https://r4epis.netlify.com/outbreaks/) and [four survey -templates](https://r4epis.netlify.com/surveys/) available. These +Sitrep has outbreak templates and survey templates available. These templates will generate the following: 1. A word document with the situation report @@ -71,8 +63,12 @@ templates will generate the following: You can access the list of templates in *R Studio* by clicking (see example below): file \> New file \> R Markdown… \> From Template -![Example of how to open and save the cholera -template](https://github.com/R4EPI/R4EPIs-website/raw/master/content/welcome/images/opening_template.gif) +
+ + +
You can generate an example template by using the `check_sitrep_templates()` function: @@ -85,16 +81,24 @@ dir.create(output_dir) # view the available templates, categorized by type available_sitrep_templates(categorise = TRUE) #> $outbreak -#> [1] "ajs_outbreak" "cholera_outbreak" "measles_outbreak" -#> [4] "meningitis_outbreak" +#> [1] "ajs_intersectional_outbreak" "ajs_outbreak" +#> [3] "ajs_outbreak_recode" "cholera_intersectional_outbreak" +#> [5] "cholera_outbreak" "cholera_outbreak_recode" +#> [7] "diphtheria_intersectional_outbreak" "intersectional_outbreak_recode" +#> [9] "measles_intersectional_outbreak" "measles_outbreak" +#> [11] "measles_outbreak_recode" "meningitis_intersectional_outbreak" +#> [13] "meningitis_outbreak" "meningitis_outbreak_recode" #> #> $survey -#> [1] "mortality" "nutrition" "vaccination_long" -#> [4] "vaccination_short" +#> [1] "ebs" "mortality" +#> [3] "mortality_recode" "nutrition" +#> [5] "nutrition_recode" "vaccination_long" +#> [7] "vaccination_long_recode" "vaccination_short" +#> [9] "vaccination_short_recode" # generate the measles outbreak template in the output directory check_sitrep_templates("measles_outbreak", path = output_dir) -#> [1] "C:\\Users\\alexf\\AppData\\Local\\Temp\\Rtmpcv1H8d/sitrep_example" +#> [1] "C:\\Users\\spina\\AppData\\Local\\Temp\\RtmpGQiM5O/sitrep_example" # view the contents list.files(output_dir, recursive = TRUE) From 590c61b8af4c79af57e296b3f635738fd0b94f57 Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:32:29 +0100 Subject: [PATCH 5/9] also the readme md --- README.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.Rmd b/README.Rmd index 1ecccf3d..5dcf6727 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,10 +16,10 @@ knitr::opts_chunk$set( # Sitrep -[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) +[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing) [![CRAN status](https://www.r-pkg.org/badges/version/sitrep)](https://CRAN.R-project.org/package=sitrep) -[![Codecov test coverage](https://codecov.io/gh/R4EPI/sitrep/branch/master/graph/badge.svg)](https://codecov.io/gh/R4EPI/sitrep?branch=master) -[![R build status](https://github.com/R4EPI/sitrep/workflows/R-CMD-check/badge.svg)](https://github.com/R4EPI/sitrep/actions) +[![R-CMD-check](https://github.com/R4EPI/sitrep/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/R4EPI/sitrep/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/R4EPI/sitrep/graph/badge.svg)](https://app.codecov.io/gh/R4EPI/sitrep) ```{r introduction-hunk, child="man/rmdhunks/introduction.Rmd"} From 22d47ab8d943e2b37707cb7b9f7586438444ba33 Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:42:12 +0100 Subject: [PATCH 6/9] updating documentation --- .Rbuildignore | 2 ++ .gitignore | 2 ++ DESCRIPTION | 13 ++++++------- man/rmdhunks/introduction.Rmd | 16 +++++++--------- man/sitrep-package.Rd | 8 +++++--- vignettes/Background.Rmd | 4 ++-- 6 files changed, 24 insertions(+), 21 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index b050673d..35706e96 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,5 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^doc$ +^Meta$ diff --git a/.gitignore b/.gitignore index 37529589..aa2c45af 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ README.html inst/rmarkdown/templates/*/skeleton/*.xlsx docs +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index 994031b7..665db75a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Type: Package Package: sitrep -Title: Report templates and helper functions for applied epidemiology +Title: Report Templates And Helper Functions For Applied Epidemiology Version: 0.2.3 Authors@R: c(person(given = "Alexander", @@ -38,13 +38,13 @@ Authors@R: role = "fnd")) Description: A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically - loads companion packages: epitabulate (for epidemiological tables), epidict - (for data dictionaries), epikit (for epidemiological utilities), and apyramid - (for age-sex pyramids). Simply load sitrep to access all functions from the - ecosystem. + loads companion packages, including epitabulate (for epidemiological tables), + epidict (for data dictionaries), epikit (for epidemiological utilities), + and apyramid (for age-sex pyramids). Simply load sitrep to access all + functions from the ecosystem. License: GPL-3 BugReports: https://github.com/R4EPI/sitrep/issues -URL: https://github.com/R4EPI/sitrep, +URL: https://github.com/R4EPI/sitrep/, https://r4epi.github.io/sitrep/ Depends: R (>= 3.2) @@ -110,4 +110,3 @@ Collate: 'sitrep-package.R' 'check_templates.R' 'metapackage_functions.R' - diff --git a/man/rmdhunks/introduction.Rmd b/man/rmdhunks/introduction.Rmd index c910eebd..ad9d746e 100644 --- a/man/rmdhunks/introduction.Rmd +++ b/man/rmdhunks/introduction.Rmd @@ -2,11 +2,12 @@ The goal of {sitrep} is provide report templates for common epidemiological surveys and outbreak reports. The package further contains helper function that standardize certain analyses. -While templates are primarily for MSF analyses - they have been setup to be as -generic as possible for use by the general applied epidemiology community. +While templates are primarily for Medecins Sans Frontieres analyses - they have +been setup to be as generic as possible for use by the general applied +epidemiology community. -**Detailed information about the project and the templates can be found at .** -A reference website for the functions in {sitrep} can be found at . +**Detailed information about the project, the templates and functions in {sitrep} +can be found at .** {sitrep} includes a number of other *R* packages which facilitate specific analysis: [{epitabulate}](https://r4epi.github.io/epitabulate): Tables for epidemiological analysis @@ -27,13 +28,10 @@ To install **sitrep** from GitHub you must first install the **remotes** package remotes::install_github("r4epi/sitrep") ``` -If you are getting errors, check the [frequently asked questions](https://r4epis.netlify.com/faq/). - ## Available templates -Sitrep has [four outbreak templates](https://r4epis.netlify.com/outbreaks/) and -[four survey templates](https://r4epis.netlify.com/surveys/) available. These -templates will generate the following: +Sitrep has outbreak templates and survey templates available. These templates +will generate the following: 1. A word document with the situation report 2. A plain text markdown document (for conversion to other formats such as HTML or PDF) diff --git a/man/sitrep-package.Rd b/man/sitrep-package.Rd index d20703d1..75a322f7 100644 --- a/man/sitrep-package.Rd +++ b/man/sitrep-package.Rd @@ -4,16 +4,16 @@ \name{sitrep-package} \alias{sitrep} \alias{sitrep-package} -\title{sitrep: Report templates and helper functions for applied epidemiology} +\title{sitrep: Report Templates And Helper Functions For Applied Epidemiology} \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} -A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages: epitabulate (for epidemiological tables), epidict (for data dictionaries), epikit (for epidemiological utilities), and apyramid (for age-sex pyramids). Simply load sitrep to access all functions from the ecosystem. +A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including epitabulate (for epidemiological tables), epidict (for data dictionaries), epikit (for epidemiological utilities), and apyramid (for age-sex pyramids). Simply load sitrep to access all functions from the ecosystem. } \seealso{ Useful links: \itemize{ - \item \url{https://github.com/R4EPI/sitrep} + \item \url{https://github.com/R4EPI/sitrep/} \item \url{https://r4epi.github.io/sitrep/} \item Report bugs at \url{https://github.com/R4EPI/sitrep/issues} } @@ -35,6 +35,8 @@ Other contributors: \itemize{ \item Annick Lenglet [contributor] \item Neale Batra [contributor] + \item Applied Epi Incorporated [copyright holder] + \item Medecins Sans Frontieres Operational Centre Amsterdam [funder] } } diff --git a/vignettes/Background.Rmd b/vignettes/Background.Rmd index 1b2fc80f..7e8ea2ec 100644 --- a/vignettes/Background.Rmd +++ b/vignettes/Background.Rmd @@ -20,7 +20,7 @@ knitr::opts_chunk$set( ## Origin -Applied Epi Tools originated out of the R4epis project. +The Sitrep ecosystem originated out of the R4epis project. R4epis started in 2018 as a partnership between Médecins Sans Frontières ([MSF](https://www.artsenzondergrenzen.nl/)) and the R for Epidemics Consortium ([RECON](http://www.repidemicsconsortium.org/)). In 2021, [Applied Epi](https://appliedepi.org/) was contracted by MSF to finalise @@ -50,7 +50,7 @@ Analysis of survey data ## Funding -R4epis was initially funded through the [Sapling Nursery](https://msf.org.uk/sapling-nursery), +R4epis was initially funded through the [Sapling Nursery](https://msf.org.uk/sapling-nursery/), an MSF internal innovation fund for new projects that aim to improve the medical care MSF provides. This funding was secured by Annick Lenglet and Amrish Baidjoe. In 2021, MSF Operational Centre Amsterdam awarded Applied Epi with a contract to From 593d5e9c1863a495180e6a746972029dfa551730 Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:42:30 +0100 Subject: [PATCH 7/9] update license --- LICENSE.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index d7e80d3b..107cb55b 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -553,7 +553,7 @@ and each file should have at least the “copyright” line and a pointer to where the full notice is found. - Copyright (C) 2019 Zhian N. Kamvar, Annick Lenglet + Copyright (C) 2019 Applied Epi Incorporated This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -573,7 +573,7 @@ Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: - sitrep Copyright (C) 2019 Zhian N. Kamvar, Annick Lenglet + sitrep Copyright (C) 2019 Applied Epi Incorporated This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details. From 6aba1bc47ad462d9037e01059a5d2bf11dbeed8c Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 20:45:06 +0100 Subject: [PATCH 8/9] add branches to codecov pr gha --- .github/workflows/test-coverage.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 0ab748d6..eb448e9c 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -4,6 +4,7 @@ on: push: branches: [main, master] pull_request: + branches: [main, master] name: test-coverage.yaml From be91dd64ec666231082a4c629a8eb831afd35f04 Mon Sep 17 00:00:00 2001 From: Alex Spina Date: Wed, 5 Nov 2025 21:13:04 +0100 Subject: [PATCH 9/9] temporarily comment out epidict::msf_dict_rename_helper while waiting on cran --- R/metapackage_functions.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/metapackage_functions.R b/R/metapackage_functions.R index 7605b8ca..0ab65a46 100644 --- a/R/metapackage_functions.R +++ b/R/metapackage_functions.R @@ -393,7 +393,7 @@ ignore_unused_imports <- function() { epidict::dict_rename_helper epidict::gen_data epidict::msf_dict - epidict::msf_dict_rename_helper + # epidict::msf_dict_rename_helper epidict::read_dict epikit::add_weights_cluster epikit::add_weights_strata