On the efficacy of restoration in stream networks: comment and critique

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." <br><br>Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). This is due to issues with experimental design, improper use of statistical analyses, and discrepancies between written methods and what was actually conducted. Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, restoration, and metacommunity ecology. <br>These are the corrected data provided by Christopher M. Swan and Bryan L. Brown (Swan and Brown 2017), and are deposited here for ease of the reader. <br> If the data are re-used, please cite the proper source: 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>Note: this is the final version of the R code and associate workspace uploaded prior to submitting the comment paper to bioRxiv. Previous versions of this fileset will have a different R code file that will yield different results. Previously, I assumed Swan and Brown (2017) appropriately used an ANOVA; however, I later determined the ANOVAs conducted by Swan and Brown (2017, 2018) were improper as they violated test assumptions. I therefore switched from Type I to Type III sums of squares and used transformations on response variables. This final version has additional analyses of taxonomic diversity to accompany the analyses of taxonomic richness. For any questions regarding differences between filesets, please do not hesitate to contact me.<br>