This year there is a mega-meeting (relatively) of paleo-societies in San Francisco. This is the 46th annual meeting for the Palynological Society (AASP-TPS), but also the annual meeting for Dino10, the Canadian Association of Palynologists (CAP), the North American Micropaleontology Section of SEPM (NAMS), and Commission Internationale de la Microflore du Paléozoïque (CIMP).
At this meeting I’ll be working with Eric Grimm and Simon Brewer to help run a workshop on the use of paleoecological databases in quantitative research. In particular we focus on the Neotoma Paleoecological Database, and the package neotoma for R. I’ve been revising the package since I first publicized it here, and it does some really amazing things now , so it would be great to train people to use it (particularly early-career researchers!) and get feedback for improvement.
In particular, we would like to point out that it is possible to sign up for only the second day, and we would encourage people to join us for the round-table discussion (see italicized section below). We are very interested in hearing about analytic needs from paleoecological researchers. What sorts of tools would you like to see developed that don’t currently exist?
Here’s the announcement from the AASP meeting page:
Dates and Times: Pre-Conference
Part 1: Saturday 19 October (9:00am-5:00pm)
Part 2: Sunday 20 October (9:00am-5:00pm)
Eric C. Grimm is Chair of Botany and Director of the Landscape History Program at the Illinois State Museum. He is the developer of Tilia and is a PI on the Neotoma project.
Simon Goring is a Postdoctoral Research Associate in the Department of Geography at the University of Wisconsin–Madison. He is developing the Neotoma API R package.
Simon C. Brewer is Assistant Professor in the Geography Department at the University of Utah.
This workshop will provide training in the use of various software packages with application to palynology, with emphasis on the Neotoma Paleoecology Database, but also including Tilia and the R package neotoma. The workshop will be held over two days, and persons can register for both days or only the introductory session on Saturday. Both days of the workshop will include lecture material and hands-on computer work with actual paleoecological data. The first day of the workshop will be geared toward users with limited experience, who are hoping to use paleoecological data at a broad spatial or temporal scale to improve their understanding of the Pliocene and Quaternary. The second day will go further into data manipulation and end with a roundtable discussion meant to spur further software and data capabilities. On both days of the workshop, time will be allotted for participants to work with their own data. Individuals interested in participating in only the more advanced session and round table discussion are asked to contact the workshop organizers before registering for only the second day to be sure that they have sufficient experience to skip the first-day, introductory session.
Neotoma is a multiproxy paleodatabase for the Pliocene and Quaternary that includes the North American Pollen Database, as well as other fossil datasets including diatoms, ostracodes, charcoal, vertebrate fauna, and geochemical data. The accessibility and broad scale of Neotoma data provides an excellent opportunity for researchers. The aim of this workshop is to help develop skills that will take researchers from data exploration to data exploitation. On the first day of the workshop participants will learn how to search and acquire multiple data types using standard web tools, and to browse the data using online mapping functions.
On the first day of the workshop participants will also become familiar with Tilia, a program well known to many palynologists for plotting pollen diagrams. The first day of the workshop will provide training on the use of Tilia for data entry, metadata entry, age-model construction, cluster analysis, and construction and editing of pollen diagrams. Workshop participants will use the most recent version of Tilia, learning how to use the basic functions and the newer capabilities, including Tilia’s new capability to interface with Neotoma. On the second day of the workshop participants will continue to work with both Tilia and Neotoma.
Neotoma provides an API (Application Programming Interface) to the database. The API allows developers and programmers to gain remote access to the database without having to download the entire database. These capabilities will be demonstrated; however, most users will access the database using software tools that automatically utilize the API.
The workshop will also introduce an R package that utilizes the Neotoma API. R is a popular open-source software environment for statistical analysis and graphing. The workshop will provide a general introduction to R, focused on paleoecological data, including capabilities for mapping, spatio-temporal analysis, transfer functions, graphing, and ordination. However, the focus of this workshop will be the R package for obtaining data from the Neotoma database and undertaking some basic analysis.
The second day of the workshop will conclude with a round-table discussion focusing on the analytical needs of paleoecologists, sources of confusion, and opportunities for the future development of additional analytic tools, and software packages.
What to bring: Participants should bring a laptop computer that can run Windows programs. A training edition of the latest version of Tilia will be distributed at the workshop, so participants should have administrative rights to install new software on their laptops. Participants should have downloaded and installed R, and the program RStudio. Both are free to download and work on multiple platforms. Workshop participants will receive more detailed instructions prior to the workshop to help them get started with R and Rstudio, and we will endeavor to accommodate all skill levels from novice to advanced.