The Countdown to 2030 Vaxx app: a Shiny app for immunization coverage and inequalities from a country's routine health facility data. Users load and check the data, choose denominators, analyse coverage, dropout, inequality, targets and equity at national and subnational level, and build Word, PowerPoint and PDF reports. In English, French and Portuguese.
It runs inside DataSuite (through the countdown-analytics extension) or on its own in R. How this package fits with the others, and how a release reaches users: countdown-analytics/docs/ARCHITECTURE.md.
install.packages("cd2030.vaxx", repos = c("https://damurka.r-universe.dev", "https://cloud.r-project.org"))
cd2030.vaxx::run_app() # prints (runs) the app
cd2030.vaxx::run_app(selected_file = "data.xlsx", language = "fr")
run_app() returns a Shiny app object; printing it or shiny::runApp() runs it. Its arguments default to the
environment variables DataSuite sets when it launches the app:
| Argument | Environment variable | |
|---|---|---|
selected_file |
CDSUITE_SHINY_SELECTED_FILE |
the file the user picked: facility data (.xls, .xlsx, .dta) or a saved dataset (.rds); NA for none |
language |
CDSUITE_SHINY_LOCALE |
"en", "fr" or "pt"
|
app_name |
CDSUITE_SHINY_NAME |
the name in the header |
app_version |
CDSUITE_SHINY_VERSION |
the version in the header; defaults to this package's version |
... |
passed to shiny::shinyApp()'s options (e.g. port) |
In DataSuite nothing needs installing by hand: DataSuite installs this package when the extension is installed and updates it when the extension is updated.
| Section | Pages |
|---|---|
| Start | Introduction (inst/intro), Load Data (the wizard, from cd2030.core, with this app's options: vaxx_wizard_options()) |
| Data quality | reporting rate, completeness, internal consistency, outliers, overall score, remove years, adjustment, adjustment changes |
| Denominators | assessment, selection |
| Analysis | national and subnational coverage, inequality, targets, equity; the Bayesian coverage model (penta3, measles1) |
| Reports | the report builder |
Every page is shared with the RMNCAH app and lives in cd2030.core (R/ui-*.R); what makes it the Vaxx app is its
settings:
| File | What |
|---|---|
R/run_app.R |
run_app(): the indicator group (vaccine), the app's config (options(cd2030.config = ...): the vaccine indicators each shared page shows, dropout indicators, adjustment k-factors, no maternal pages), translations, the nav tree, then cd2030.core::cd_app()
|
R/pages.R |
vaxx_pages(): every page (id, UI, server, title, section, help topic, report) |
R/page-0_upload_data.R |
this app's Load Data options |
inst/translation/translation.json |
the app's own texts (merged over datasuite.ui's and cd2030.core's with cd_translations()) |
inst/intro/0_intro_<lang>.md |
the Introduction page |
app.R |
runs the app from this folder (see below); not part of the package |
data-reference.json |
what DataSuite's AI tools read; a copy lives in the extension, not part of the package |
shiny::runApp() # from this folder: app.R loads the source with pkgload::load_all()
devtools::check() # must stay at 0 errors, 0 warnings, 0 notes
app.R uses pkgload::load_all() when it finds DESCRIPTION next to it, otherwise the installed package. To try a
change to cd2030.core or datasuite.ui at the same time, install that package locally first (for cd2030.core:
devtools::install(quick = TRUE, upgrade = FALSE, dependencies = FALSE), so its Remotes: don't reinstall
datasuite.ui from GitHub).
Keep R/ ASCII (\uXXXX escapes in strings): R CMD check warns otherwise. A page this app needs that RMNCAH could use
too belongs in cd2030.core, not here.
Version: in DESCRIPTION, add a NEWS.md entry, devtools::check() clean.vX.Y.Z, push main and the tag. r-universe builds it within about an hour (instantly with its GitHub
app installed).package.version for Vaxx in the extension's package.json and release the extension.