cardinal_rlib

By Rudolf Cardinal ([email protected]).

This is an inelegant bunch of files containing miscellaneous code for use with R and Stan.

You can source the latest version from Github. For example, to "source" the miscstat.R file from R, you can do this:

source("https://raw.githubusercontent.com/RudolfCardinal/rlib/master/miscstat.R")

and a copy should also be at https://egret.psychol.cam.ac.uk/rlib, as in:

source("https://egret.psychol.cam.ac.uk/rlib/miscstat.R")

Clearly these should be built into a proper R package at some stage.

Notes on requiring/attaching/loading packages

As per https://r-pkgs.org/dependencies-mindset-background.html, the main concepts for users are (a) "load", and (b) "load + attach". Attaching puts the package on the search path, so you can call somefunc() rather than somepackage::somefunc(). But library-style code should not mess with the search path.

To load only, use loadNamespace() to throw an error upon failure, or requireNamespace() to return FALSE. (The "load + attach" equivalents are library() and require(), respectively.)

User-mode code can simplify installation like this:

if (!require("pacman")) install.packages("pacman")
pacman::p_load(
    data.table,
    patchwork
    # ...
)

To show packages:

library()  # show install packages (system and user)
(.packages())  # show loaded packages; see ?.packages
loadedNamespaces()  # show loaded namespaces

Note that a package doesn't have to be loaded explicitly to be called via package::function() notation, it appears (empirically); that was a surprise to me. It works on the command line: for example, if you have the "survival" package installed but not loaded, and then type survival::<tab>, survival will appear in a subsequent loadedNamespaces() call. But even this works as a script:

#!/usr/bin/env Rscript

print(loadedNamespaces())
survival::cluster(5)
print(loadedNamespaces())

However, install.packages(...) does not add to loadedNamespaces(). In contrast, pacman::p_load(...) does.

Therefore, our quasi-library code does this for user convenience:

tmp_require_package_namespace <- function(...) {
    packages <- as.character(match.call(expand.dots = FALSE)[[2]])
    for (p in packages) if (!requireNamespace(p)) install.packages(p)
}
tmp_require_package_namespace(
    data.table,
    patchwork
    # ...
)
rm(tmp_require_package_namespace)

# Could also use: packages <- sapply(substitute(...()), deparse)
# cat("Loaded namespaces:\n"); print(loadedNamespaces())
# cat("Attached packages:\n"); print(.packages())