pradeeshwarrj/pamflow ? reverse-engineered prompt

Build me an R package for an end to end passive acoustic monitoring workflow that takes raw field recordings and turns them into useful ecological outputs with one config file and a few simple function calls.

I want it to help organize and check audio from common recorders, batch run BirdNET detections, clean and merge those detections, let me review and validate results in a Shiny app, and then build occupancy histories, activity summaries, richness and diversity metrics, and report tables for downstream modeling. It should also include a soundscape analysis path that computes common acoustic indices like ACI, ADI, AEve, Bio, H, M, and NDSI, with daily profiles and HTML summary reports.

Please make it feel like a real analysis tool for researchers, with a setup flow, a sample project I can try right away, clear config driven defaults, and good documentation and examples. If you need to check current package docs or best practices online, go ahead and do that.