I am passionate about making my science reproducible and open, and firmly believe that this improves the quality of my work and increases the speed at which science as a whole can progess. All of my GitHub repositories can be seen at https://github.com/DevonDeRaad.
Empirical projects
For each of my empirical projects, I strive to maintain a dedicated GitHub repository that documents all code and raw data inputs used to generate results in a comprehensive and user-friendly manner. Below I list a few of my recent empirical projects and link to the dedicated repository for each project which contains all code and raw input files necessary to completely reproduce the results:
https://github.com/DevonDeRaad/towhees.uces - DeRaad, D. A., Applewhite, E. E., Tsai, W. L., Terrill, R. S., Kingston, S. E., Braun, M. J., & McCormack, J. E. (2023). Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in Pipilo towhees. Evolution. 77(3), 852-869.
https://github.com/DevonDeRaad/todiramphus.radseq - DeRaad, D. A., McCullough, J.M., DeCicco, L.H., Hime, P.M., Joseph, L., Andersen, M.J., & Moyle, R. G. Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers. Molecular Ecology (in review).
https://github.com/DevonDeRaad/aph.rad - DeRaad, D. A., McCormack, J. E., Chen, N., Peterson, A. T., & Moyle, R. G. (2022). Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays. Systematic Biology, 71(6), 1453-1470.
Software development
I have also developed two open-source R packages, both of which are available via CRAN and Github. I use both of these packages regularly to maintain fast and well-documented data analysis pipelines for my empirical projects. These packages are: SNPfiltR and RADstackshelpR. Each is designed for streamlining the processing of next-gen (i.e., Illumina) DNA datasets using R. Each is extensively documented with user tutorials that show reccommended uses. They are also detailed below:
SNPfiltR
SNPfiltR is a
RADstackshelpR
is
Tutorials
In the Fall of 2022, I led an extended weekly workshop for students at the University of Kansas learning to analyze RADseq data for the first time. I developed an 11 week curriculum complete with weekly tutorials walking the students through every step in the process from getting comfortable working on the command line and a high-performance computing cluster, to performing phylogenetic and population genetic analyses on their filtered datasets at the end of the semester. All course materials are publicly available at: https://github.com/DevonDeRaad/Fall.2022.RAD.workshop.