Software

Open-source tools I’ve built or co-built, mostly for the Neotoma Paleoecology Database community. Everything here is free to use.

neotoma2

An R package for finding, downloading, and analyzing data from the Neotoma Paleoecology Database. It follows a tidyverse-style approach, so Neotoma records drop straight into your usual R workflows.

DataBUS

A toolkit that validates and bulk-uploads community datasets into Neotoma. Every file is checked against the Neotoma data model before upload, and uploads run as a single all-or-nothing transaction, so a site is never left half-loaded. I’ve built DataBUS workflows for ostracode and speleothem (SISAL) data, and I’m currently building one for ancient and environmental DNA.

neotoma2faire (in development)

Exports ancient and environmental DNA data from the Neotoma APIs into the FAIRe (FAIR eDNA) metadata standard, so eDNA records can be shared in an open, machine-readable format.

Neotoma infrastructure

  • Dataset landing pages with DOIs for every Neotoma dataset: data.neotomadb.org
  • Public database snapshots and a Docker image, so anyone can run Neotoma locally: Neotoma snapshots

Publications

Dominguez Vidaña, S., & Goring, S. J. (2023). neotoma2: An R package to access data from the Neotoma Paleoecology Database. Journal of Open Source Software, 8(91), 5561. https://doi.org/10.21105/joss.05561