To ensure reproducibility, you can run dyngen in a docker container. dynverse/dyngen contains all necessary packages to run dyngen from start to finish. Ideally, you would take a look at the latest tag published on docker hub and replace any mentions of
dynverse/dyngen:<latest digest>, to make sure you’re always using the exact same version of dyngen.
To run the container, you can use the following command.
docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true -v `pwd`:/home/rstudio/workdir dynverse/dyngen
Keep this window open, and open up a browser and go to 127.0.0.1:8787. Open up the file
getting_started.R for a small example on how to run a dyngen simulation.
The command can be dissected as follows.
docker run \ # remove container after use --rm \ # specify which port rstudio server uses -p 127.0.0.1:8787:8787 \ # disable authentication because I'm lazy -e DISABLE_AUTH=true \ # mount the current working directory in the rstudio home folder # so you will see it right away when rstudio starts -v `pwd`:/home/rstudio/workdir \ # specify which container to run dynverse/dyngen
If a newer version of the container has been released, you can update it by running the following command.
docker pull dynverse/dyngen
To build this docker container from scratch, run the following command.
docker build -t dynverse/dyngen -f docker/Dockerfile .
GITHUB_PAT should be an environment variable corresponding to the Personal Access Token created by following this tutorial.