Daniel C. Reuman, University of Kansas, [email protected]
Max Castorani, University of Virginia
Kyle Cavanaugh, UCLA
Lawrence W. Sheppard, Marine Biological Association of the United Kingdom
Jonathan Walter, University of Virginia
Tom Bell, UCSB and Woods Hole Oceanographic Institution

This repository can be used to reproduce the analyses behind the paper "How environmental drivers of synchrony interact" and to recompile the latex of the paper. Data are also included in the repository. As of June 2023, the paper has now been accepted for publication in the journal Ecography.

If you want to run the unit tests of the function used, make your R working directory equal to the Code directory of the repository and run testthat::test_dir("."). This should take less than 1 minute. You may have to install an R version or some R packages that you don't have to get these tests to pass. Keep in mind these tests were run when the paper was written, with versions R and R studio and R packages which were current around then (see below), so no guarantees if a lot of time has passed since then. You can always run the code on the (now) old version of R and the packages and it should work then, but you'll have to set up a (now) old version of R with (now) old packages yourself. Yes, I have heard of the checkpoint package, Microsoft has now abandoned MRAN so this is not a way toward reproducibility anymore.

To run the codes that reproduce the analyses of the paper, make your R working directory equal to the Code directory of the repository and run source("main.R"). If all dependencies are in place (see below), this will pull data from the Data directory and create results and then put them in the Results directory. All results are regenerated except Fig. 3, which was produced separately by Max Castorani on his machine, based on data exported by the script Kelp_AnalysisStep_MakeMapFigDat.R which is invoked by main.R. It was not considered necessary to embed Max's scripts into this workflow because Fig. 3 is purely descriptive, intended solely to introduce the kelp system; main results are not based on Fig. 3.

To recompile the main text and supporting information of the paper, knit the Latex/Sweave files Paper.Rnw and SupMat.Rnw, which are in the Paper directory. These files will import results from the Results directory and will create two pdfs in the Paper directory. You may have to do several knits, alternating between the two files, to get all the links to work.

R, R studio, a setup that can compile Sweave documents. The right versions of everything may be required - see below.

I used R version 4.3.0 running on Ubuntu 18.04, and R studio version 2023.03.0+386.

Set your R studio up so there is a button near the top that compiles .Rnw files into pdfs.

The packages I used were current around the time of R version 4.3.0. Specifically: matrixcalc, version 1.0-6; wsyn, version 1.0.4; ncf, version 1.3-2; latex2exp, version 0.9.6; testthat, version 3.1.9; mvtnorm, version 1.2-2; shape, version 1.4.6; graphics, version 4.3.0; stats, version 4.3.0; parallel, version 4.3.0.

You may have to install the versions of R, R studio, and the packages listed above to get the code to run if a lot of time has passed since publication.

The code and paper compilation process was tested by Reuman on Ubuntu 18.04 using R version 4.3.0 and R studio version 2023.03.0+386. It has not been tested on other machines. We have endeavored to list all dependencies we can think of above, but we have only run the code on Reuman's machine, so we cannot guarantee that additional dependencies will not also be needed on other machines. This repository is intended to record a workflow, and is not designed or tested for distribution and wide use on multiple machines. It is not guaranteed to work on the first try without any hand-holding on arbitrary computing setups.

Knitting the Sweave code automatically produces a lot of 'intermediate' files. Files ending in .tex are the converted documents from .Rnw including all the R code output and the rest (files ending .log, .aux, .lof, .lot, .toc and .out ) are intermediate files that pdflatex uses to keep track of various parts of the document. Some of these can be useful for diagnosing problems, if any.

This study was partly funded by the U.S. National Science Foundation (NSF) through linked NSF-OCE awards 2023555, 2023523, 2140335, and 2023474 to M.C.N.C, K.C.C., T.W.B, and D.C.R., respectively; and by NSF-Math Bio award 1714195 to D.C.R.; and by support to D.C.R. from the James S. McDonnell Foundation, the Humboldt Foundation, and the California Department of Fish and Wildlife Delta Science Program. This project used data developed through the Santa Barbara Coastal Long Term Ecological Research project, funded through NSF-OCE award 1831937. The authors thank Vadim Karatayev, Maowei Liang, Kyle Emery, Nat Coombs, Adeola Adeboje and Ethan Kadiyala for helpful discussions. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation or the other funders.