Sources for: Avoiding tipping points in fisheries management through Gaussian Process Dynamic Programming
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This directory contains the
.Rmd files for the manuscript and
supplement. These files use functions from the R package from this
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
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,
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.
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
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
- A LaTeX environment
nonparametric-bayespackage from github, including all packages in the DESCRIPTION file (by default suggested packages are not installed).
: 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.