This workshop is designed to provide users of the Neotoma Database with an overview of the new neotoma2 R package, and its use in obtaining data from the Neotoma Paleoecology Database.
At the end of this workshop, users will understand the following concepts:
- How data is structured within Neotoma and in the R package
- How to search for data in space and time
- How to extract summary objects from individual sites and collections of sites
- How to manipulate data to add new chronologies
Online resources for users include links embedded within the agenda, as well as:
- Online, interactive slides (open the “Slides” folder): https://bit.ly/EPDSlides
- An online version of RStudio built for this workshop: https://bit.ly/EPDRstudio
- The code repository for the workshop: https://github.com/NeotomaDB/EPD_binder
Install the R package:
install.packages('devtools')
devtools::install_github('NeotomaDB/neotoma2')
Neotoma maintains an online community on Slack that includes a channel for help using R and Neotoma (#it_r). Come join our community: https://bit.ly/3PT8zuP
This allows us to better help you during the workshop and in the future.
- The Neotoma Database Manual: https://open.neotomadb.org/manual/
- The
neotoma2GitHub Repository: https://github.com/neotomadb/neotoma2
4 Hours (1pm - 4:50pm)
| Time | Topic | Overview | Link |
| 1:00 - 1:15pm | Introductions | Run through each individual’s profile quickly, say hi & introduce ourselves. | https://bit.ly/EPDIntros |
| 1:15 - 1:20pm | Why neotoma2 | Explaining why we’ve moved to a new package, rather than updating the `neotoma` R package. | https://docs.google.com/presentation/d/1UhIJ3HJskE9ymmFZ109ktsKKuqzW21JZc8fiWQLkyZw/edit?usp=sharing |
| 1:20 - 2:00pm | A simple workflow | https://open.neotomadb.org/EPD_binder/simple_workflow.html | |
| 1:20 - 1:30 | Simple Site Search | How to search for sites by space & name. | |
| 1:30 - 1:35 | Independent Searching | Individuals will use the geoJSON site to select an area, perform a search and plot the results. Paste the image on your personal slide. | |
| 1:35 - 1:40 | Quick Debrief | One or two people, what did you find? | |
| 1:40 - 1:50 | Searching for Datasets and Filtering | How to extract datasets by dataset type & see summary information about records. | |
| 1:50 - 2:00pm | Independent filtering | Users will filter by time, space &cetera. | |
| 2:05 - 2:10pm | Quick debrief | What do you need from Neotoma? | |
| 2:10 - 2:30pm | Samples & Stratigraphic plotting | How to pull them from sites/datasets. Key features, filtering. | Intro to taxonomic harmonization is in the simple_workflow.html |
| 2:30 - 3:00pm | Break | ||
| 3:00 - 3:20 | Spatial Analysis | Using climate data from WorldClim rasters, examine taxon distributions in climate space | |
| 3:20 - 3:30 | Independent Breakout 1 | See instructions in the slide | Link removed for online version. |
| 3:30 - 4:50 | Working with chronologies | https://open.neotomadb.org/EPD_binder/complex_workflow.html | |
| 3:30 - 3:40 | Welcome back & looking at chronologies/chroncontrols | ||
| 3:40 - 3:50 | Independent time | ||
| 3:50 - 4:00 | Building the Chronology | ||
| 4:00 - 4:10 | Adding the Chronology | ||
| 4:10 - 4:30 | Independent Breakout 2 | Groups of 3 – Work through some stuff | |
| 4:30 - 4:50 | Debrief | ||