cd2030.rmncah

The Countdown to 2030 RMNCAH app: a Shiny app for the end-to-end analysis of a country's routine health facility data for reproductive, maternal, newborn, child and adolescent health. Users load and check the data, choose denominators, analyse coverage, equity, mortality, service use and the health system, 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 and run

install.packages("cd2030.rmncah", repos = c("https://damurka.r-universe.dev", "https://alkemalab.r-universe.dev",
                                            "https://cloud.r-project.org"))
cd2030.rmncah::run_app()                                   # prints (runs) the app
cd2030.rmncah::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.

What is in it

Section	Pages
Start	Introduction (`inst/intro`), Load Data (the wizard, from cd2030.core, with this app's options: `rmncah_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, continuum of care, inequality, targets, equity; mortality (institutional, mapping, completeness); service utilization (data quality, national, subnational, MCH curative index); health system (national, subnational, comparison, private sector); Bayesian coverage model (national, subnational)
Reports	the report builder

Most pages are shared with the Vaxx app and live in cd2030.core (R/ui-*.R). This package holds only what is RMNCAH's:

File	What
`R/run_app.R`	`run_app()`: the indicator group (`rmncah`), the app's config (`options(cd2030.config = ...)`: which indicators each shared page shows, adjustment k-factors, reporting-rate indicators...), translations, the nav tree, then `cd2030.core::cd_app()`
`R/pages.R`	`rmncah_pages()`: every page (id, UI, server, title, section, help topic, report)
`R/page-*.R`	the RMNCAH-only pages: continuum of care, mortality, service utilization, MCH curative index, health system, private sector, and 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`, `docs-index.json`	what DataSuite's AI tools read; copies live in the extension, not part of the package

The Bayesian pages need bayescoveragemodel and bayescoveragedeploy (suggested by cd2030.core, from https://alkemalab.r-universe.dev).

Develop

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. Column names used unquoted in dplyr code go in R/globals.R.

A page RMNCAH and Vaxx both need belongs in cd2030.core, not here.

Release

Bump Version: in DESCRIPTION, add a NEWS.md entry, devtools::check() clean.
Commit, tag vX.Y.Z, push main and the tag. r-universe builds it within about an hour (instantly with its GitHub app installed).
DataSuite users get it at the next update of the countdown-analytics extension. If they must have this version, raise package.version for RMNCAH in the extension's package.json and release the extension.