OOS 40-2 - Implementing a reproducible, open source framework in ecological monitoring

Friday, August 12, 2016: 8:20 AM
Grand Floridian Blrm G, Ft Lauderdale Convention Center
Monica Granados, Department of Biology, McGill University, Montreal, QC, Canada
Monica Granados, McGill University

Background/Question/Methods

The Earth Stewardship Initiative (ESI) is an innovative project that facilitates interdisciplinary collaboration between managers, community leaders, designers and ecologists. In 2014, the ESI convened in Sacramento California in conjunction with the ESA Annual General Meeting. Through a series of workshops and lectures, ecologists worked with American River Parkway conservation professionals to integrate scientific methodology into restoration projects and monitoring programs. The 2014 project generated designed experiments to monitor pollinators, invasive species and highlighted the importance of collaboration between ecologists and decision makers. Here, we extend the concept integrating novel methodology into urban landscapes by introducing reproducible, open frameworks into ecological monitoring.

Like many conservation authorities, the Toronto Region and Conservation authority is tasked with delivering regular reports on the status of fish communities in their jurisdictions. From the manual entry of data, to exporting data into statistical software and finally the output of figures each step in the production of reports requires hours of manual input across multiple software platforms and departments. To streamline this process I developed an R Markdown script and a Shiny application that integrate R script to perform the statistical analyses and outputs the results in a formatted PDF that ingrates both text and figures.

Results/Conclusions

The implementation of a reproducible produciton process using open source software streamlined the creation of reports by integrating workflows. The R Markdown script seamlessly pulls data collected by the field monitoring group from the database and when complied produces updated statistical tests and figures in a formatted PDF. This methodology eliminates the manual data transfer between collection, analyses and formatting in a reproducible framework that integrates any new data. Further the method is cost-effective as it uses cross-platform, open source software that does not require the purchase of proprietary software. The open platform also allows other conservation authorities to ingrate this methodology in their programs.

Conceivably without initiatives like the ESI, interactions between ecologists, conservation professionals, designers and managers are limited along with the opportunity to transmit knowledge in both directions. It is imperative then to foster these programs among ecologists to ensure the innovations we make in our discipline propagate and are integrated in real world solutions to the pressing ecological questions we are facing.