seroCOP-api

A minimal Plumber API that runs brms/Stan fits for seroCOP on the server and returns JSON + base64 plots. This supports the hybrid approach recommended by Alix: browser for UI, server for model fitting.

Endpoints

• GET /health: basic health check and seroCOP version
• POST /fit: multipart/form-data upload with csv file and options

POST /fit parameters

• csv (file): CSV dataset
• infected_col (string, default infected): binary outcome column
• tire_col (string, optional): biomarker/titre column; if omitted, first numeric column is chosen
• chains (int, default 2): Stan chains
• iter (int, default 1000): iterations per chain

Run locally

R -e "pr <- plumber::plumb('plumber.R'); pr$run(host='0.0.0.0', port=8001)"

Or with Docker.

Docker

The included Dockerfile uses rocker/r-ver and installs system deps + R packages.

# Build
docker build -t serocop-api:latest ./seroCOP-api
# Run
docker run --rm -p 8001:8001 serocop-api:latest

Example cURL

curl -X POST \
  -F csv=@examples/example_data.csv \
  -F infected_col=infected \
  -F chains=2 \
  -F iter=1000 \
  http://localhost:8001/fit

Integrate with seroCOP-web

• In the browser, detect if the dataset requires server fitting (i.e., brms/Stan). If yes, POST to /fit and render returned plot and metrics.
• For small demos, keep the client-side simplified glm path; otherwise offload to this API.