install_packages.R

options(repos = "https://cran.rstudio.com/")

if (!require("pacman")) install.packages("pacman")

# isntall linelist
pacman::p_load_gh("reconhub/linelist", dependencies = TRUE)

# install dsr
pacman::p_load_gh("cran/dsr", dependencies = TRUE)

# install sf
pacman::p_load_gh("r-spatial/sf", dependencies = TRUE)

# install BiocManager
pacman::p_load(BiocManager)

# install Biobase
BiocManager::install("Biobase", update = TRUE, ask = FALSE)

# install ggtree
BiocManager::install("ggtree", update = TRUE, ask = FALSE)

# install epicontacts
pacman::p_load_gh("reconhub/epicontacts@timeline", dependencies = TRUE)

# install sitrep
remotes::install_github("r4epi/sitrep")

pacman::p_load(
  bookdown,
  downlit,
  xml2,
  here,
  dplyr,
  incidence2,
  sessioninfo,
  janitor,
  skimr,
  kableExtra
)