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Appendix S1. References for the R packages. For version numbers please refer to the nearest CRAN http://www.r-project.org/

Appendix S2. Journals with 30 or more hits retrieved through an ISI-search for multivariate methods, comprising 1401 of the 2037 total publications (636 hits are thus not shown). Abbreviations of the journals follow ISI standards.

Appendix S3. Results of the log-ratio test (type III sum of squares) of the GLM (Poisson distribution of errors) testing the dependence of the proportion of studies (see Fig. 1) published in the five manually reviewed journals on ordination method, journal and year, including all two-way interactions (LR=log ratio, DF=degrees of freedom; residual degrees of freedom=528).

Appendix S4. Diversity in ordination methods over the years: (a) total proportion of applications for a given year and diversity indices; (b) mean values calculated over all years for all journals and split down to journal level (significance level of Spearman correlations with time are indicated as asterisks: P&0.05 ?*?; P&0.01 ?**?; P&0.001 ?***?).

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