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Sources for: Avoiding tipping points in fisheries management through Gaussian Process Dynamic Programming

<!-- Manuscript code is run automatically any time changes are made to this repository. The badge above summarizes the status and contains links to further details. -->

This directory contains the .Rmd files for the manuscript and
supplement. These files use functions from the R package from this
repository (nonparametric-bayes) but also several additional R packages
and other software which are responsible for the parametric comparisons,
as well as software responsible merely for the formatting to go from
.Rmd to a .pdf file (e.g. knitr, pandoc, LaTeX).

All of these additional dependencies means that rebuilding the
manuscript from scratch means more software to install and more
points of failure. To help you get started, we provide a copy
of the software environment we use in this paper as a Docker
container. If you'd rather not worry about the installation details,
Install Docker
on your laptop or a user-friendly cloud

The badge above is automatically generated when the manuscript
is rebuilt on a remote server. This provides a convenient way
to confirm that everything is still working.

Docker Quickstart

Install Docker on your laptop or server. Mac & Windows users should then launch the installed boot2docker app to access the Docker terminal. Linux users just open any terminal. Then run:

docker run -d -p 8787:8787 cboettig/nonparametric-bayes

This downloads the computational environment necessary and launches RStudio-server to interact with it. Point your browser to:


Mac and Windows users should replace localhost with the IP address returned by boot2docker ip. Log in with user: rstudio and password: rstudio. See rocker-org Wiki for more details like custom passwords.

You can now open manuscript.Rmd or supplement.Rmd files in RStudio and run the code interactively or compile the pdfs from scratch. See RStudio's rmarkdown for details.

Local Installation requirements

  • RStudio (includes pandoc)
  • A LaTeX environment
  • The nonparametric-bayes package from github, including all packages in the DESCRIPTION file (by default suggested packages are not installed).

[1]: this link provides $10 credit to Digital Ocean; enough to run a 1GB instance for a month. Disclosure: If you subsequently become a Digital Ocean customer the authors receive a credit for the referral.

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