Abstract
The open source and free programming language R is a phenomenal mechanism to address a multiplicity of challenges in ecology and evolution. It is also a complex ecosystem because of the diversity of solutions available to the analyst.Packages for R enhance and specialize the capacity to explore both niche data/experiments and more common needs. However, the paradox of choice or how we select between many seemingly similar options can be overwhelming and lead to different potential outcomes.There is extensive choice in ecology and evolution between packages for both fundamental statistics and for more specialized domain‐level analyses.Here, we provide a checklist to inform these decisions based on the principles of resilience, need, and integration with scientific workflows for evidence.It is important to explore choices in any analytical coding environment—not just R—for solutions to challenges in ecology and evolution, and document this process because it advances reproducible science, promotes a deeper understand of the scientific evidence, and ensures that the outcomes are correct, representative, and robust.
Highlights
Data are a critical form of evidence in ecology and evolution—not the only form and an important contribution
We provide a checklist to inform these decisions based on the principles of resilience, need, and integration with scientific workflows for evidence
Methods in Ecology and Evolution for instance had the highest reported proportionate usage of all journals recently examined in a recent study (Lai et al, 2019)
Summary
2015; Perring, Erickson, & Brancalion, 2018) and in how we do science with the open science movement growing (Nosek et al, 2015; Tennant et al, 2016), increasing availability of data (Hampton et al, 2013), and increasing accountability of science to society (Sequeira, Bouchet, Yates, Mengersen, & Caley, 2018; Sutherland, Fleishman, Mascia, Pretty, & Rudd, 2011). R has become the lingua franca with over 60% of 60,000 articles in these domains reporting its use by 2017 (Lai, Lortie, Muenchen, Yang, & Ma, 2019) This is a phenomenal opportunity for collaborative science, community building, and new forms of shared methodological literacy (Knuth, 1992). At least three packages were returned per instance but typically many, many more with up to 2,876 packages listed for a single concept (Figures 1 and S1) This does not necessarily indicate that each package will provide the desired function but that the documentation mentions this term (similar to bibliometric searches of peer-reviewed publications wherein mentions vs relevancy are not always directly related). Inspection of the 100 most frequent terms used to describe the functions provided by the top 10 ecology and evolution
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