R/epi_project_setup.R

In AntonioJBT/episcout: Quickly Clean, Explore and Visualise Large Epidemiological Datasets

# TO DO: needed? cean up, covnert to function?, etc

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# Generic renv management
# Copy to new project directory
# No input
# Creates / updates in project directory:
  # - A folder 'renv' in the project directory, and
  # - A lockfile called 'renv.lock' in the project directory
  # - .gitignore
  # - .Rbuildignore
  # - .Rprofile

# Local cache of data on the filesystem, located at:
  # - "~/Library/Caches/org.R-project.R/R/renv"

# See:
  # vignette("renv")
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# Directory locations
# getwd()
# dir(path = normalizePath('xx'), all.files = TRUE)

project_name <- 'xx'
projects_dir <- '~/Documents/work/xx'

project_root <- sprintf('%s/%s', projects_dir, project_name)
print(project_root)
setwd(project_root)
getwd()

# code_loc <- "~/Documents/work/devel/xx"
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# Import libraries
library(renv)
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# Check current state
# system and project libraries
.libPaths()

# See which packages are available in each library:
lapply(.libPaths(), list.files)
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# Get started with an environment:
# TO DO: add if so that if there's a lockfile already it uses that by default
renv::init() # requires interaction on the console if it finds an existing renv.lock

# Install, load libraries, update (manually):
# TO DO: run checks before, update automatically (?)
renv::install()
renv::update() # checks for updates and asks interactively

# Update the lock file with current libraries:
renv::snapshot() # also needs user confirmation

# Check for renv Sync Issues with
renv::status()

# Restore to the state in renv.lock file at project root:
renv::restore()

# Clear the existing renv setup
unlink("renv", recursive = TRUE)
unlink("renv.lock")

# Reinitialize renv
renv::init() # will symlink for efficiency all global R library packages already present

# Reinstall any project-specific packages
# install.packages(c("dplyr", "ggplot2"))  # Replace with your project's packages

# Snapshot the environment to save the state
renv::snapshot()

# TO DO: complete cycle (?)
# To
# renv::restore()
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# renv might interrupt console needing user input (eg for CLI running)


# Options:
# renv::status()
# renv::load() instead of load()

# disable temporarily if batch running, e.g.:
    # Disable renv prompts
    # Sys.setenv(RENV_CONFIG_PROMPT_ENABLED = "FALSE")
    # Load the .rdata.gzip file
    # load("xxx.rdata.gzip")
    # Optionally re-enable prompts if desired
    # Sys.unsetenv("RENV_CONFIG_PROMPT_ENABLED")


# Ensure No Automatic Reload coming from .Rprofile, e.g.:
# if (file.exists("renv/activate.R")) {
#   source("renv/activate.R")
# }

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# The end:
sessionInfo()
# q()
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