On the relativity of stream restoration and the need for reproducible research: comment

R code and associated data for a comment on a paper by Christopher Swan and Bryan Brown titled "Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration." I provide a commentary and critique of the paper by offering a re-analysis of the data, with hypotheses and interpretation in the context of stream, metacommunity, and restoration ecology. I show that results can depend on the sites and concomitant restoration treatments. I highlight limitations of the experimental design and how liberal usage of restoration without considering how individual and combinations of treatments could affect the study system. Moreover, I show that the efficacy of restoration is relative, dependent on which sites are included in the analysis. Importantly, I show that the results presented in the original paper and erratum are not reproducible. I evaluate where discrepancies occur and provided explanations for these deviations. I also discuss potential errors in analysis by Swan and Brown (2017, 2018), including the deviations in written statistical methods and what was actually conducted. Given that analytical scripts are not always required or even provided alongside manuscripts, readers assume what has been described in the manuscript is what was done in the actual analysis. Unfortunately, this is not the case for Swan and Brown (2017, 2018), and should be of concern for ethical and reproducible ecological research.<br>These data were provided with the initial manuscript by Christopher M. Swan and Bryan L.Brown (Swan and Brown 2017), and are also provided here for ease of the reader.<br>If the data are re-used, please cite the proper sources:Swan, C. M., and B. L. Brown. 2017. Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 27:2209-2219.<br>Swan, C. M., and B. L. Brown. 2018. Erratum for: Metacommunity theory meets restorations: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 28: 1370-1371.<br>