README.md

vaxedemic

Optimal global allocation of vaccinations during a pandemic

Build Status

Testing link to vignette, if needed.

Running an example simulation

  1. Clone this repository to a local directory (henceforth referred to as local_dir).
  2. If running locally, make a subdirectory in the repository directory called outputs. The simulation outputs will be saved here.
  3. If running on the cluster, make a directory in the network drive (henceforth referred to as remote_dir). Make two subdirectories in remote_dir, called outputs and data respectively. Copy everything in the data directory of this repository into remote_dir/data.
  4. If running on the cluster, and you have not previously submitted an R job to the cluster, setup the interface between R and the cluster by following these instructions
  5. Choose a username (doesn't have to be your DIDE username). Edit R/cluster_tools.R so that your didehpc options (as in the instructions) are configured in get_user_options. Make sure that wd and package_dir are set to remote_dir and local_dir respectively.
  6. Edit scripts/example.R, replacing user <- "ayan" with your username, and package_dir <- "~/Documents/vaxedemic/" with your local directory.
  7. Set cluster <- TRUE near the top of scripts/example.R if running on the cluster, otherwise replace with cluster <- FALSE.
  8. Set run_fixed <- TRUE near the top of scripts/example.R if running for a fixed set of parameters, otherwise replace with run_fixed <- FALSE to run for many combinations of parameters.
  9. Source scripts/example.R.

Installation

devtools::install_github("jameshay218/vaxedemic")

To do to package structure, if needed

  1. Integrate with Travis
  2. Write test cases
  3. Write full vignettes

License

GPL-3 © James Hay <[email protected]>.



jameshay218/vaxedemic documentation built on July 29, 2018, 12:43 p.m.