RT Journal Article
SR Electronic
T1 Developing an automated iterative near-term forecasting system for an ecological study
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 268623
DO 10.1101/268623
A1 Ethan P. White
A1 Glenda M. Yenni
A1 Shawn D. Taylor
A1 Erica M. Christensen
A1 Ellen K. Bledsoe
A1 Juniper L. Simonis
A1 S. K. Morgan Ernest
YR 2018
UL http://biorxiv.org/content/early/2018/08/27/268623.abstract
AB Most forecasts for the future state of ecological systems are conducted once and never updated or assessed. As a result, many available ecological forecasts are not based on the most up-to-date data, and the scientific progress of ecological forecasting models is slowed by a lack of feedback on how well the forecasts perform.Iterative near-term ecological forecasting involves repeated daily to annual scale forecasts of an ecological system as new data becomes available and regular assessment of the resulting forecasts. We demonstrate how automated iterative near-term forecasting systems for ecology can be constructed by building one to conduct monthly forecasts of rodent abundances at the Portal Project, a long-term study with over 40 years of monthly data. This system automates most aspects of the six stages of converting raw data into new forecasts: data collection, data sharing, data manipulation, modeling and forecasting, archiving, and presentation of the forecasts.The forecasting system uses R code for working with data, fitting models, making forecasts, and archiving and presenting these forecasts. The resulting pipeline is automated using continuous integration (a software development tool) to run the entire pipeline once a week. The cyberinfrastructure is designed for long-term maintainability and to allow the easy addition of new models. Constructing this forecasting system required a team with expertise ranging from field site experience to software development.Automated near-term iterative forecasting systems will allow the science of ecological forecasting to advance more rapidly and provide the most up-to-date forecasts possible for conservation and management. These forecasting systems will also accelerate basic science by allowing new models of natural systems to be quickly implemented and compared to existing models. Using existing technology, and teams with diverse skill sets, it is possible for ecologists to build automated forecasting systems and use them to advance our understanding of natural systems.