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The course outline and manual for a workshop to teach paleoecologists how to use the neotoma package for R.
Course Authors & Instructors: Simon Goring - goring@wisc.edu Simon Brewer
Thanks to: Eric Grimm, Jessica Blois, Michael Anderson & Brian Bills.
This workshop is intended to provide a basic introduction to the R computing environment through a workflow that focuses on paleoecological analysis using the newly developed neotoma package for R. Workshop participants will find site data using the Neotoma Paleoecological Database, download data and plot and perform basic analysis on the resulting datasets.
Users are expected to:
- Bring their laptops to the workshop
- Have R installed on their laptop with a suitable editor. We recommend RStudio.
- Users may also bring their own datasets if interested.
The R user and development community has contributed to R over time to the point that it is an incredibly powerful tool for analyis, and provides an opportunity for open and reproducible research. The paleoecological community has a history of data sharing, including the COHMAP Project, North American Pollen Database, North American Modern Pollen Database and Neotoma. With the development of the neotoma package for R we hope to include both data and data processing in this spirit of sharing.
Recent paleoecological work such as Goring et al. (2012), Gill et al. (2013) and Goring et al. (2013) have explicitly included both R code and data to allow for reproducible work. As our analytic methods increase in complexity, Methods sections become hard pressed to describe all the choices we make in analysis. In addition, the recent, highly publicized errors in high-profile research, make the case for providing reproducible code all the more compelling.
So lets all get on the reproducible science train using R and neotoma and our own intellectual curiosity!
This is the second of a two day workshop. The last hour of the day will be given over to a discussion of the analytic needs of the paleoecological community.
| Time | Topic | Link |
|---|---|---|
| 8:30 | Introduction to R, RStudio and R workflows | Link |
| 9:00 | Web services & APIs | Link |
| 9:30 | Basic searches with neotoma |
Link |
| 10:00 | What does a pollen object look like? | Link |
| 10:30 | Manipulating pollen data | Link |
| 11:30 | Eating some food | Link |
| 12:30 | Spillover from pre-lunch | Link |
| 1:30 | Free time for discovery | |
| 2:30 | Quantitative round table |
If you have some familiarity in R already we hope that the workflow we've designed will give ou enough freedom to play around with other features while we walk through some of the more fundamental R concepts. If you are new to R we hope that the code that you take some time to familiarize yourself with R before the workshop. There are a number of excellent tutorials available online.
| Tutorial | Link | Description |
|---|---|---|
| An Introduction to R | The introduction to R, a large PDF with extensive indexing. | |
| A Very Short Introduction to R | I've only just found this and it loks good. The examples all use RStudio. | |
| Intro to R | website | It's from the University of Wisconsin so it must be good. |
| Try R | online course | By O'Reilly Press, an online course with a web interface. |
Navigation - Home - Intro to R - Web Services & APIs - Basic Search - Pollen Objects - Manipulating Pollen