Running EpiSewer with docker

This vignette describes how to use EpiSewer in a docker container to avoid installation of CmdStan on your system. The image is available as a package from the github container registry.

Step 1: Install the EpiSewer package

Install the EpiSewer package from github as usual:

remotes::install_github("adrian-lison/EpiSewer", dependencies = TRUE)

Step 2: Pull the docker image

Pull the docker image from the github container registry (make sure that your docker daemon is running!):

EpiSewer::sewer_pull_docker()

Step 3: Load the package

library(EpiSewer)

Step 4: Define docker as backend

We will use this backend during model fitting as shown in step 5.

docker_backend <- model_stan_opts(use_docker = TRUE)

Step 5: Fit the model with fit_opts

We here use example data and assumptions for SARS-CoV-2 in Zurich, which are included in the package.

ww_result <- EpiSewer(
  data = ww_data_SARS_CoV_2_Zurich,
  assumptions = ww_assumptions_SARS_CoV_2_Zurich,
  fit_opts = set_fit_opts(
    sampler = sampler_stan_mcmc(
      iter_warmup = 500, iter_sampling = 500, chains = 4, seed = 42
      ),
    model = docker_backend
  )
)

Step 6: Inspect results as usual

For example, plot the estimated reproduction number:

plot_R(ww_result)