install-r-packages.r

#!/usr/bin/env Rscript

# List of packages to ensure are installed
required_packages <- c("renv")

# Check and install required packages
new_packages <- required_packages[!sapply(required_packages, requireNamespace, quietly = TRUE)]
if (length(new_packages) > 0) {
  install.packages(new_packages)
}

packages <- c(
  "AER@1.2-14",
  "BH@1.87.0-1",
  "BiocManager@1.30.25",
  "DBI@1.2.3",
  "FNN@1.1.3",
  "IRkernel@1.3.2",         # required for jupyter R kernel
  "Matrix@1.7-1",
  "R.methodsS3@1.8.2",
  "R.oo@1.27.0",
  "R.utils@2.12.3",
  "RCSF@1.0.2",
  "RColorBrewer@1.1-3",
  "RCurl@1.98-1.16",
  "RNetCDF@2.9-2",
  "RcppProgress@0.4.2",
  "assertthat@0.2.1",
  "bibtex@0.5.1",
  "bindrcpp@0.2.3",
  "broom@1.0.7",
  "crosstalk@1.2.1",
  "data.table@1.16.4",
  "devtools@2.4.5",
  "dichromat@2.0-0.1",
  "e1071@1.7-16",
  "forcats@1.0.0",
  "future@1.32.0",
  "gdtools@0.4.1",
  "geoR@1.9-4",
  "geometry@0.5.0",
  "geosphere@1.5-20",
  "ggplot2@3.5.1",
  "ggthemes@5.1.0",
  "globals@0.16.3",
  "gstat@2.1-2",
  "haven@2.5.4",
  "hdf5r@1.3.11",
  "here@1.0.1",
  "hms@1.1.3",
  "htmlwidgets@1.6.4",
  "intervals@0.15.5",
  "jsonlite@1.8.9",
  "units@0.8-5",
  "leafem@0.2.3",
  "leaflet@2.2.2",
  "leafpop@0.1.0",
  "leafsync@0.1.0",
  "learnr@0.11.5",
  "lfe@3.1.0",
  "linprog@0.9-4",
  "listenv@0.9.1",
  "lpSolve@5.6.23",
  "lubridate@1.9.4",
  "lwgeom@0.2-14",
  "magic@1.6-1",
  "manipulateWidget@0.11.1",
  "mapdata@2.3.1",
  "mapproj@1.2.11",
  "mapview@2.11.2",
  "markdown@1.13",
  "matrixStats@1.4.1",
  "modelr@0.1.11",
  "ncdf4@1.23",
  "ncmeta@0.4.0",
  "nlme@3.1-166",
  "ottr@1.5.1",
  "packrat@0.9.2",
  "pander@0.6.5",
  "pbdZMQ@0.3-13",
  "png@0.1-8",
  "proj4@1.0-14",
  "proto@1.0.0",
  "pryr@0.1.6",
  "rapportools@1.1",
  "raster@3.6-30",
  "rdrobust@2.2",
  "readr@2.1.5",
  "readxl@1.4.3",
  "rematch@2.0.0",
  "remotes@2.5.0",
  "repr@1.1.7",
  "reprex@2.1.1",
  "reshape@0.8.9",
  "reticulate@1.40.0",
  "rjson@0.2.23",
  "rlas@1.8.0",
  "rlist@0.4.6.2",
  "rpart@4.1.23",
  "rsconnect@1.3.3",
  "satellite@1.0.5",
  "selectr@0.4-2",
  "sp@2.1-4",
  "spacetime@1.3-2",
  "spatialreg@1.3-6",
  "spatstat@3.3-0",
  "spatstat.data@3.1-4",
  "spdep@1.3-8",
  "splancs@2.01-45",
  "stargazer@5.2.3",
  "stars@0.6-7",
  "summarytools@1.0.1",
  "svglite@2.1.3",
  "testit@0.13",
  "tidync@0.4.0",
  "tidyr@1.3.1",
  "tidyverse@2.0.0",
  "tmap@3.3-4",
  "tmaptools@3.1-1",
  "tufte@0.13",
  "utf8@1.2.4",
  "uuid@1.2-1",
  "viridis@0.6.5",
  "vroom@1.6.5",
  "whoami@1.3.0",
  "widgetframe@0.3.1",
  "withr@3.0.2",
  "xfun@0.49",
  "xts@0.14.1",

  # dplyr packages
  "dplyr@1.1.4",
  "arrow@18.1.0",
  "dbplyr@2.5.0",
  "dtplyr@1.3.1",
  "nycflights13@1.0.2",
  "Lahman@12.0-0",
  "RMariaDB@1.3.3",
  "RPostgres@1.4.7",
  "RSQLite@2.3.9",
  "fst@0.9.8",
  # /dplyr packages

  # publishing packages
  "blogdown@1.19",
  "rticles@0.27",
  "xaringan@0.30",
  # /publishing packages

  # https://github.com/berkeley-dsep-infra/datahub/issues/4907
  # "Fall '23 and beyond"
  "mosaicData@0.20.4",

  # From https://github.com/berkeley-dsep-infra/datahub/issues/5496
  # pol sci 3, spring 2024 and into the future
  "estimatr@1.0.4",

  # From https://github.com/berkeley-dsep-infra/datahub/issues/3757
  # econ 140, fall 2022 and into the future
  "ipumsr@0.8.1",

  # https://github.com/berkeley-dsep-infra/datahub/issues/6545
  # ENVECON 118, Spring 2025
  "foreign@0.8-87",
  "ggthemes@5.1.0",
  "gridExtra@2.3",
  "lmtest@0.9-40",
  "magrittr@2.0.3",
  "margins@0.3.28",
  "multcomp@1.4-26",
  "openxlsx@4.2.7.1",
  "quantmod@0.4.26",
  "QuantPsyc@1.6",
  "qwraps2@0.6.1",
  "sandwich@3.1-1",
  "stats@4.5.0",

  # DH-446, Econ 140, Spring 2025
  "wooldridge@1.4-3"

)

renv::install(packages)

# Posit Package Manager currently has no binary BioConductor packages.
BiocManager::install("rhdf5")
BiocManager::install("Rhdf5lib")