Create R_package_basics.R

packages/R_package_basics.R

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+# Show the current library paths where R looks for packages
+.libPaths()
+
+# List all installed packages (data frame of package metadata)
+installed.packages()
+
+
+###############################################
+# Changing and resetting library paths
+###############################################
+
+# Save the current library search paths so we can restore them later
+old_libpaths <- .libPaths()
+
+# Temporarily set the library path to a temp folder (not recommended long-term)
+.libPaths(tempdir())
+
+# Change library path to the current working directory
+.libPaths(getwd())
+
+# Restore the original library paths
+.libPaths(old_libpaths)
+
+# Prepend a custom folder to the library paths
+.libPaths(c("C:/Users/Martin.Brown1/Desktop/OldCBTI/WorkBTI/RDemo/Test Folder",
+            old_libpaths))
+
+
+###############################################
+# Installing packages into different locations
+###############################################
+
+# Install DoseFinding into the *first* library in .libPaths()
+install.packages("DoseFinding")
+
+# Install 'stringr' into a specific library folder, using a custom CRAN mirror,
+# and without installing dependencies
+install.packages(
+  "stringr",
+  lib = "C:/Users/Martin.Brown1/Desktop/OldCBTI/WorkBTI/RDemo/Test Folder2",
+  repos = "https://cran.ma.imperial.ac.uk/",
+  dependencies = FALSE
+)
+
+# Overwrite library paths to look only in Program Files
+# (R likely has no write access here)
+.libPaths("C:/Program Files")
+
+# Install a package from a source tarball (older version from CRAN Archive)
+install.packages(
+  "https://cran.r-project.org/src/contrib/Archive/DoseFinding/DoseFinding_1.3-1.tar.gz",
+  repos = NULL, type = "source"
+)
+
+# Remove a previously installed package
+remove.packages("DoseFinding")
+
+
+##################################################
+# Demonstrating function masking and namespaces
+##################################################
+
+words <- c("First","Second","Third")
+
+# Calling str_length() *before* loading stringr — will fail unless stringr loaded
+str_length(words)
+
+library(stringr)
+# Now str_length() works because stringr is attached
+str_length(words)
+
+# Detach the package completely
+detach("package:stringr", unload = TRUE)
+
+# Using the function explicitly via namespace, without attaching the package
+stringr::str_length(words)
+
+
+########################################################
+# Demonstrating masking between dplyr and stats
+########################################################
+
+install.packages("dplyr")
+
+library(dplyr)
+
+View(iris)
+
+# dplyr::filter() filters rows
+filter(iris, Sepal.Length > 7)
+
+# Detach stats (usually not needed – just for demonstration)
+detach("package:stats", unload = TRUE)
+
+# Re-load stats
+library(stats)
+
+# Now filter() may refer to stats::filter (time-series filter!), not dplyr
+filter(iris, Sepal.Length > 7)   # likely error or unexpected result
+
+# Help for filter will show the stats version
+?filter
+
+# Use the fully qualified dplyr function
+dplyr::filter(iris, Sepal.Length > 7)
+
+
+##################################################################
+# Checking versions and session info
+##################################################################
+
+# Get the installed version of ggplot2
+packageVersion("ggplot2")
+
+# Display detailed information about R, OS, loaded packages
+sessionInfo()
+
+
+################################################################
+# Mini-exercise: read a CSV file with readr
+################################################################
+
+# Point the library path to a custom folder
+.libPaths("C:/Users/Martin.Brown1/Desktop/OldCBTI/WorkBTI/RDemo/Test Folder3")
+
+# Install readr into that folder
+install.packages("readr")
+
+library(readr)
+
+?read_csv
+
+# Read a CSV file using readr
+MAI <- read_csv(
+  file = "C:/Users/Martin.Brown1/Desktop/OldCBTI/WorkBTI/RDemo/MAI.csv"
+)
+
+
+#################################################################
+# Installing from GitHub with 'remotes'
+#################################################################
+
+install.packages("remotes")  # install once
+
+# Install a specific tagged GitHub release
+remotes::install_github(
+  "insightsengineering/teal.reporter",
+  ref = "v0.5.0"
+)
+
+
+#################################################################
+# Installing from GitHub with 'pak'
+#################################################################
+
+install.packages("pak")  # install once
+
+# Install the same tagged release, using pak's syntax
+pak::pkg_install("github::insightsengineering/teal.reporter@v0.5.0")
+
+
+##################################################################
+# Minimal renv demo — no scanning of thousands of files
+##################################################################
+
+# Set the library path to a clean folder for the renv demo
+.libPaths("C:/Users/Martin.Brown1/Desktop/OldCBTI/WorkBTI/RDemo/Test Folder3")
+
+install.packages("renv")
+
+# Initialize renv WITHOUT scanning the project for dependencies
+renv::init(bare = TRUE)
+
+# Install a package inside the renv environment
+install.packages("stringr")   # or any package you like
+
+# Snapshot the exact state of the renv library to renv.lock
+renv::snapshot()
+
+# Show dependencies that renv thinks are in the project
+renv::dependencies()