[]

Neotoma Current R Workshop

Simple Workflow: North American Diatoms

Mapping Diatoms and Water Chemistry in North America

A repository to host the interactive neotoma2 R workshops. This repository will always be set up for the most recent/current Neotoma Workshop. All past workshops will be archived in the Neotoma Workshops repository.

This repository is built with the structure required to serve the content through an interactive, online RStudio session using Binder. Clicking the Binder link will open RStudio in the user's browser.

Currently, this repo hosts the Neotoma Diatom Workshop to be delivered at Drexel University, Philadelphia, Pennsylvania, USA, on November 10-12, 2026. The R sessions are on November 10 and 11. Because the workshop is held in the United States, the examples focus on diatoms in the USA and the wider North American region.

The workshop material is:

• simple_workflow.Rmd: A Simple Workflow: North American Diatoms. Search for diatom sites by name and location, filter by dataset type, download the samples of one Pennsylvania diatom record, then look up the diatom names in GBIF with one call (and harmonize them yourself in a spreadsheet), draw a stratigraphic diagram, and follow the change in diatom families through time in Barnegat Bay.
• maps_neotomaWorkshop.Rmd: Mapping Diatoms and Water Chemistry in North America. Map the diatom, diatom surface sample and water chemistry sites of North America, see which diatom sites also have water chemistry, load an aggregate dataset from a spreadsheet of IDs, map lake pH, join diatoms with pH, and compare Aulacoseira with July and February temperatures from WorldClim. Everything reads from the cached files in data/.

To access the content for this Workshop, click the badge below:

Contributors

This is an open project and contributions are welcome from any individual. All contributors to this project are bound by a code of conduct. Please review and follow this code of conduct as part of your contribution.

• Socorro Dominguez Vidana

• Nick Hoffman

• Simon Goring

• Zoe Kerrich, Drexel University (Academy of Natural Sciences): the diatom mapping workflow, the North America polygon and the aggregate-dataset inventory that this workshop material is adapted from.

How to use this repository

This repository contains a simple workflow that shows how to access data and perform relatively simple analysis. These workflows may be modified for content (e.g., focusing on different dataset types or geospatial contexts).

Users may clone this workshop and modify the content, but be aware that the Binder links are specific to this repository, and must be modified through the users' own Binder setup.

• Dockerfile defines the Binder/Docker image. It copies only the files the workflow reads.
• install.r defines the R packages that are installed in the Binder environment. The workshop uses the development version of neotoma2 from GitHub (NeotomaDB/neotoma2, branch dev). After the new release reaches CRAN, install.r can go back to install.packages("neotoma2").
• data/ holds pre-downloaded Neotoma results, so the workflow does not depend on live API calls during the workshop.

To run the workflows locally, install the packages listed in install.r and open the .Rmd files in RStudio.