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>本数据集包含用于评述Christopher Swan与Bryan Brown题为《集合群落理论与修复：隔离如何调控生态群落对河流修复的响应》（Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration）论文的R代码及配套数据。 Swan与Brown（2017）近期以集合群落理论框架为基础，探讨了河流修复对河流群落的影响。他们结合源头溪流与主干溪流样地，评估了河流网络内的空间位置如何调控无脊椎动物群落的修复效果。表面上，其假说得到了部分验证：修复对源头溪流的影响更为显著，修复河段的无脊椎动物分类丰富度得以提升，时间变异性有所降低；然而，无论是原始论文（Swan and Brown 2017）还是后续勘误（Swan and Brown 2018），经进一步审视后其结果均存在不一致性。这一问题源于实验设计缺陷、统计分析方法使用不当，以及书面方法与实际操作之间的偏差。本研究对原始数据开展二次分析，结合河流生态学、修复生态学及集合群落生态学的研究语境提出假说并进行解读。 本次使用的校正后数据由Christopher M. Swan与Bryan L. Brown（Swan and Brown 2017）提供，上传至此以方便读者查阅。 若需复用本数据，请引用下述文献：Swan, C. M. 与 B. L. Brown. 2017. 集合群落理论与修复：隔离如何调控生态群落对河流修复的响应. 《生态学应用》（Ecological Applications）27:2209-2219。 注：本文件为提交至bioRxiv的评述论文前上传的最终版R代码及配套工作区文件。此前版本的文件集包含的R代码文件存在差异，运行后将得到不同结果。最初我曾认为Swan和Brown（2017）合理使用了方差分析（ANOVA），但后续发现其2017年与2018年研究中使用的方差分析违反了检验假设，属于不当使用。因此我将平方和类型从I型调整为III型，并对响应变量进行了转换处理。本最终版新增了针对分类多样性的分析，以配合分类丰富度分析。若对不同版本文件集间的差异存在疑问，请随时与我联系。