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Changelog

Source: NEWS.md

ntrd 0.0.1

Initial release of ntrd, the Neuropsychological Test Results Dashboard. The package provides a Shiny application — built on top of ntrs — for presenting neuropsychological test scores in a form useful for consensus diagnosis, plus an extension API for adding new data sources.

Shiny dashboard

  • shinyDashboard() launches the application. Also available from the RStudio “Addins” menu as “Neuropsychological Test Result Dashboard”.
  • Multi-panel layout built with bslib and Bootstrap 5.
  • Per-participant view with study ID selector, demographics table, and visit-date selector.
  • Asynchronous data loading for extension data (e.g. biomarkers) via mirai daemons, so the UI stays responsive while extensions fetch data in the background.

Data sources

  • Built-in CSV upload source (csv_source) for files in NACC format.
  • Built-in Demo source (demo_source) that loads ntrs::demo_data with derived variables (REYTOTAL, REYAREC, FAS, MOCACLOCK) pre-computed — useful for trying the app without real data.
  • data_nacc S7 class validates input data on construction: checks for required columns (NACCID, SEX, EDUC, BIRTHYR), enforces column types, validates SEX and visit-date values, and auto-derives VISITDATE and NACCAGE when their components are present.

Extension API

  • Third parties can register new data sources by declaring Config/ntrd/extension: true in DESCRIPTION and providing S7 methods for data_source_ui(), data_source_server(), and data_load().
  • new_data_source() constructor for defining a class that inherits from data_source.
  • discover_data_sources() scans installed packages at app startup and populates the data-source dropdown.
  • Extensions can ship additional UI panels and reactive helpers via the extras channel returned from data_source_server().
  • Extensions can optionally provide a restore function so previously entered configuration (e.g. API tokens) can be repopulated.
  • Conflict detection warns when multiple extensions define std_using_* generics with the same name.
  • Full walkthrough available in the “Extension API” vignette, with ntrdWisconsin as a complete worked example.

Tables and visualizations

  • assessment_summary_table() / mainTableModule — the main per-visit NACC T-Cog assessment summary table, rendered with gt.
  • assessment_longitudinal_table() / longTableModule — longitudinal table of scores across visits.
  • demographics_table() — compact gt demographics summary with flagging for missing or visit-to-visit-varying values.
  • prev_diagnoses_table() / prevDiagnosesModule — prior diagnoses table.
  • plotModule — interactive plotly longitudinal trend plots, one accordion panel per cognitive domain, with crosswalk pairs colored consistently and trace-visibility state surfaced back to Shiny.
  • “Generate PDF for Download” button on the main table (requires pagedown); falls back to a friendly install hint when pagedown isn’t available.

Customization

  • descriptionsModule — interactive table for editing score-region labels, upper-bound cutoffs, and fill colors. Rows can be added, edited, reordered (by upper bound), removed, or reset to defaults.
  • Sidebar option to toggle shading of plots according to descriptions.
  • Sidebar slider to adjust main-table font size.
  • “Setup” tab (methodSelectModule) for choosing standardization methods and assigning variables to cognitive domains; defaults are auto-applied when available, with a notification pointing to the Setup tab for customization.

In-app extension updates

  • check_extension_update() calls an extension’s exported ntrd_update_available() (cached for one hour by default; configurable via ttl); clear_update_cache() invalidates the cache.
  • Update banner appears in the header when a newer version of the active extension is published, with a “What’s new?” link to the extension’s NEWS.md when provided.
  • Two-stage restart cascade (install in one restart, relaunch in the next) for RStudio users; clear manual install instructions in the modal for Positron, plain R, Rscript, and the VS Code R extension, where the restart-with-command flow isn’t supported.
  • update_result S7 class formalizes the contract between extensions and the framework; validate_update_check_result() gracefully downgrades malformed results to a safe “no update” state instead of crashing the app.
  • default_github_update_available() and default_github_update_extension() factories provide ready-to-use implementations for GitHub-hosted extensions.

Infrastructure

  • MIT licensed.
  • R (>= 4.2.0).
  • CI on GitHub Actions: R-CMD-check on macOS, Windows, and Ubuntu (devel / release / oldrel-1); pkgdown site build and deploy; Codecov coverage upload.
  • shinytest2-based tests for the Shiny modules.
  • pkgdown site at https://rmtrane.github.io/ntrd/.