wsyn: Wavelet approaches to studies of synchrony in ecology - introduction to the repository of codes supporting the talk
Daniel C. Reuman, University of Kansas, reuman@ku.edu
Jonathan Walter, University of California Davis, jawalter@ucdavis.edu
This repository can be used to reproduce the analyses behind the talk ``wsyn: Wavelet approaches to studies of synchrony in ecology'' given by Jon Walter and Dan Reuman as part of the ESA/Ecological Forecasting Initiative Webinar, 5/6/24, 12:00pm EDT. The idea behind this repo is to provide the complete, reproducible workflow for all the analysis and simulations that went into the talk, as well as the latex which produced the talk slides themselves. A recording of the tlk itself can be found here https://www.youtube.com/watch?v=sxVHFwAkhdA.
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.
You may have to install an R version or some R packages
that you don't have for this to work. Keep in mind these codes were run shortly prior to when the talk was given,
on Jon's and Dan's machines, so no guarantees if a lot of time has passed since then.
We made no efforts at long-term reproducibility, but our R and package versions are listed below.
AFTER having run the R codes, to recompile the talk slides, compile the latex in talk, under the file name TheTalk.tex. You have to do this after you run R codes because the R codes generate the figures
which are then sucked up into the latex doc. Without those figures, the latex won't compile.
This is ordinary beamer latex. This can be done from within R studio if you have it configured
correctly. The pdflatex command from the ubuntu command line can also work.
R, R studio, a setup that can compile beamer latex documents. The right versions of everything may be required - see below.
Dan used R version 4.3.0 running on Ubuntu 18.04, and RStudio version 2023.03.0+386. Jon used R version 4.2.1 running on MacOS 12.7.4 and RStudio version 2023.09.1+494.
The packages we used were more or less current around the time the talk was given. Specifically:
Dan: wsyn, version 1.0.4
Jon: wsyn, version 1.0.4
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 the talk.
The code and paper compilation process was tested by Jon and Dan on their machines. 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 our machines, 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.
We acknowledge all the coauthors with whom we worked in writing the initial papers on which this work is based, and the R package wsyn.