R setup

setup.R

# If you need to, install R by visiting CRAN (https://cran.r-project.org/) and
# downloading the appropriate version for your operating system.

# Create a project folder `delphi_project` and open it.

# Open an R terminal and install the renv, pak, and rspm packages by running the
# commands below.
# * The pak package is the modern installer for R packages. Learn more at
#   https://pak.r-lib.org/.
# * The rspm package is a package manager for R that allows you to install
#   packages from the RStudio Package Manager (RSPM), where you can find
#   precompiled packages for Linux (you can ignore this if you're not on Linux).
#   This dramatically speeds up package installation time. Learn more at
#   https://cran4linux.github.io/rspm/.
# * The renv package is a package manager for R that allows you to create a
#   project-specific library of packages. This ensures that your project is
#   reproducible and that you can share your project with others without
#   worrying about package versions. Learn more at
#   https://rstudio.github.io/renv/.
install.packages(
  "pak",
  repos = sprintf(
    "https://r-lib.github.io/p/pak/stable/%s/%s/%s",
    .Platform$pkgType, R.Version()$os, R.Version()$arch
  )
)
pak::pkg_install(c("rspm", "renv"))

# Run the following code to initialize the renv package.
renv::init()

# Create a new file in the project folder called `.Rprofile` and add the
# following lines to it.
source("renv/activate.R")
# Ignore the following line if you're not on Linux.
rspm::enable()

# Restart the R session and now type the following code to install the
# dependencies for the project.
pak::pkg_install(c("epidatr", "cmu-delphi/epiprocess", "cmu-delphi/epipredict"))

# After a few minutes, you should now have all the dependencies needed to start
# working with the packages.