opensyndrome

Your R package to interact with Open Syndrome definitions!

Apply Open Syndrome Definitions (OSD) to tabular health data in R: download and cache definitions, map your dataset's columns to OSD concepts, and classify records by inclusion/exclusion criteria.

A focused R subset of open-syndrome-python, sharing the same on-disk cache (~/.open_syndrome/).

Status: early development. The classification engine is being built test-first; the public API grows one verified slice at a time.

Working now: download/cache and load definitions (os_download_definitions(), os_load(), os_list()), inspect them (os_required_fields(), os_describe(), os_validate()), map columns (os_read_profile() / os_validate_profile()), and classify (os_filter() / os_label()). Next: bundled example data and the getting-started vignette.

Usage (current API)

library(opensyndrome)

# 1. Get definitions (cached in ~/.open_syndrome/v1, shared with Python)
os_download_definitions()
os_list(disease = "Dengue", country = "United States")
dengue <- os_load("dengue_usa")          # by name, local file, or URL

# 2. See what the definition needs, then map your columns
os_required_fields(dengue)
os_describe(dengue)
profile <- os_read_profile("mapping.yaml", "ambulatory_care")
os_validate_profile(profile, my_data)    # catch mapping mistakes early

# 3. Classify
cases    <- os_filter(my_data, dengue, profile)                       # matching rows
labelled <- os_label(my_data, list(dengue = dengue, zika = zika), profile)  # a column each

A definition is a plain named list (as parsed from OSD JSON). Criteria that can't be evaluated against your columns are skipped with a warning by default; set on_unresolvable = "error" to stop instead.

Install

# install.packages("remotes")
remotes::install_github("OpenSyndrome/open-syndrome-r")

Run from source

remotes::install_deps(dependencies = TRUE)  # from the repo root
devtools::load_all()
devtools::test()

The cache lives at ~/.open_syndrome/v1 (shared with the Python package). Point it elsewhere with the OPENSYNDROME_HOME environment variable.

Contributing

Development is strictly test-driven (red → green → refactor): write the failing testthat test first, confirm it fails, then implement.

usethis::use_test("thing")   # add tests/testthat/test-thing.R
devtools::test()             # run the suite
devtools::document()         # regenerate NAMESPACE + man/ after roxygen changes

Tests live in tests/testthat/; each R/<topic>.R has a matching test-<topic>.R.