Supplement 1. Annotated R scripts and sediment core data used to investigate regime shift dynamics in a Galapagos coastal lagoon.

<h2>File List</h2><div> <p><a href="data.csv">data.csv</a> (MD5: a6d684a54a17794fa0a79c739d403b63)   Diablas lagoon diatom (%), stable carbon isotope (‰) and interpolated Ti influx data (µg.cm<sup>-2</sup>.yr<sup>-1</sup>). Four minor data handling errors have been corrected in the stable carbon isotope data from Seddon et al. 2011.</p> <p><a href="Script.R">Script.R</a> (MD5: 4b2c776d9ead3f85f9a3bb37af7a77a3)  Example R script to apply regime shift detection techniques and non-linear regressions in this study for analysis of data.csv.</p> <p><a href="STARS.R">STARS.R</a> (MD5: 99bcf013e9a5738843813b7815ce74e9)  R script required to implement Sequential T-test Analysis of Regime Shifts Algorithm (Rodionov 2004, 2006) in script.R.</p> </div><h2>Description</h2><div> <p>The supplements are designed to provide an example of the framework used to investigate regime shifts in this study. The main file script.R is annotated and split into two parts: STEP 1 investigates whether regime shifts can be identified in diatom assemblages, STEP 2 provides an example of fitting non-linear regressions on the PC1 axis of the diatom data across Regime Shift 1. This can be repeated across other time steps and other datasets (e.g., Ti influx, δ<sup>13</sup>C) in the way. A number of other packages are required, documented within the script.R file. See R documentation for more information. </p> <p>To run the script, place all data files into the same directory, open R and set the working directory to that folder. Open up the file script.R and follow the annotations (marked with #) to detect regime shifts in the diatom data and then statistically model the changes in the temporal series. </p> </div>