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Lakes, landscapes, and R: A framework for open science on freshwater cyanobacteria
Citation:
Hollister, Jeff AND Bryan Milstead. Lakes, landscapes, and R: A framework for open science on freshwater cyanobacteria. U.S. Chapter of the International Association of Landscape Ecology (US-IALE) Annual Meeting, Chicago, IL, April 08 - 12, 2018.
Impact/Purpose:
The primary impact of this work is twofold. First, it highlights efforts of openness and transparency within the Atlantic Ecology Division cyanobacteria research efforts. Second, it promotes tools developed by EPA researchers that have broad applicability across the field of ecology.
Description:
In the last several years scientific reproducibility has been a hot topic with several fields openly struggling with reproducing and replicating research results. One of the key tools to address reproducibility is the use of open source software. Increasingly in ecology, the R language for statistical computing is the open source software of choice for analysis and programming tasks. Our research group has also made the choice to invest in the use of R for our work. In this poster we share examples of how we use R to help build anopen foundation for our work on understanding how water quality, landscapes, and limnological processes interact to control cyanobacteria blooms. In particular we discuss three R packages - `lakemorpho`, `elevatr`, and `goatscape` - that we have developed to facilitate our research. The `lakemorpho` package provides the ability to more easily reproduce calculation of lake morphometry metrics. One of the data requirements for `lakemorpho` is access to elevation data. In response to this need, we developed `elevatr` to provide access to digital elevation models and point elevation estimates for anywhere in the world. Lastly, we are developing `goatscape` to provide the ability to reproducibly summarize key landscape metrics within an input landscape polygon. While these tools have direct applications to landscape and limnological research, they are more broadly conceived such that they can benefit the larger landscape ecology community and help facilitate openness and reproducibility of a variety of landscape ecological research efforts.