Search for CRAN packages by keyword/regex

Description

Inspired by my mysterious inability to remember what the RColorBrewer package is actually called. Lets you find relevant CRAN packages right from your terminal.

Usage

browse_cran(query, fuzzy = FALSE, echo = TRUE, ignore.case = TRUE)

Arguments

Details

When browse_cran() is run for the first time in a new session, it will take about 6-12 seconds to download and cache CRAN data. This only happens once per session; subsequent calls will use the cached copy.

Value

Invisibly returns a dataframe of the packages that matched the query together with their descriptions. Prints results to the console.

Examples

browse_cran("colorbrewer")  # Search by keyword

#> RColorBrewer 
#>     Provides color schemes for maps (and other graphics) designed by Cynthia 
#>     Brewer as described at http://colorbrewer2.org 
#> 
#> Redmonder 
#>     Provide color schemes for maps (and other graphics) based on the color 
#>     palettes of several Microsoft(r) products.


browse_cran("zero-inflat.*?(abund|count)")  # Search by regular expression

#> hurdlr 
#>     When considering count data, it is often the case that many more zero 
#>     counts than would be expected of some given distribution are observed.

# And five other matches...


browse_cran("network twitter api", fuzzy = TRUE)  # Order-agnostic (fuzzy) search

#> RKlout 
#>     An interface of R to Klout API v2.

Check if packages are attached

Description

Check if packages are attached

Usage

check_attached(...)

Arguments

Value

If dots is empty, a character vector of all attached packages. Otherwise, return a named logical vector where TRUE means the package is attached

Examples

## Not run: 
check_attached()

#>   [1] "librarian" "testthat"  "magrittr"  "stats" ...

check_attached(c("utils", "stats"))

#> utils stats 
#> TRUE  TRUE 

check_attached("datasets", "base", fakepkg)

#> datasets     base  fakepkg 
#>     TRUE     TRUE    FALSE 

## End(Not run)

Check if packages are installed

Description

Check if packages are installed

Usage

check_installed(...)

Arguments

Value

If dots is empty, a character vector of all installed packages. Otherwise, return a named logical vector where TRUE means the package is installed.

Examples

## Not run: 
check_installed()

#>   [1] "addinslist"  "antiword" " ape"  "assertthat"  ...

check_installed(c("utils", "stats"))

#> utils stats 
#> TRUE  TRUE 

check_installed("datasets", "base", fakepkg)

#> datasets     base  fakepkg 
#>     TRUE     TRUE    FALSE 

## End(Not run)

Check if packages are installed or attached

Description

Check if packages are installed or attached

Usage

check_pkg_status(..., status, use_list = FALSE)

Arguments

Value

If dots is empty, a character vector of package names. Otherwise, return a named logical vector where TRUE means the package is installed or attached, depending on the value of status.

Collapse a vector

Description

I use this internally for turning a vector of package names into a string.

Usage

collapse_vec(..., wrap = "'", collapse = ", ", unique = TRUE)

Arguments

Value

A string.

Examples

## Not run: 
collapse_vec(month.abb)
#> [1] "'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec'"

## End(Not run)

Is the 1st 'dots' arg a character vector with length > 1?

Description

Is the 1st 'dots' arg a character vector with length > 1?

Usage

dots1_is_pkglist(...)

Arguments

Value

TRUE if ..1 is a vector or list with length > 1.

Examples

## Not run: 
dots1_is_pkglist()

#> [1] FALSE

dots1_is_pkglist("hello", "hey", "hi")

#> [1] FALSE

dots1_is_pkglist(c("hello", "hey"), "hi")

#> [1] TRUE

dots1_is_pkglist(c(hello, hey), "hi")

#> [1] FALSE

# A common programming scenario:
pkg_list <- c("only_one_package")
dots1_is_pkglist(pkg_list)

#> [1] TRUE

## End(Not run)

Did the user pass arguments inside dots?

Description

Did the user pass arguments inside dots?

Usage

dots_is_empty(...)

Arguments

Value

TRUE (dots is empty) or FALSE (dots is not empty).

Examples

## Not run: 
is_dots_empty(package, names, here)

#> [1] FALSE

## End(Not run)

How many items are in dots?

Description

How many items are in dots?

Usage

dots_length(...)

Arguments

Value

An integer

Examples

## Not run: 
dots_length(package, names, here)

#> [1] 3

## End(Not run)

Turn a list of words into a fuzzy regex

Description

A fuzzy regex is one that will match search terms in any order by using PERL lookaround. This is very slow, but often worth the cost to get more complete results.

Usage

fuzzy_needle(vec)

Arguments

Value

A string where each word has been wrapped as a lookaround term.

Examples

## Not run: 
fuzzy_needle("network centrality")
#> [1] "(?=.*network)(?=.*centrality)"

## End(Not run)

Assert that a URL is complete and valid

Description

Assert that a URL is complete and valid

Usage

is_valid_url(string)

Arguments

Details

The regex I use is "@stephenhay" from https://mathiasbynens.be/demo/url-regex because it's the shortest regex that matches every CRAN mirror at https://cran.r-project.org/mirrors.html.

Value

A logical value, TRUE if the URL is valid, FALSE if otherwise.

Examples

## Not run: 
is_valid_url("http://rstudio.com")

## End(Not run)

Changing and viewing the package search paths

Description

View and edit the list of folders that R will look inside when trying to find a package. Add an existing folder, create and add a new folder, or shuffle a folder to the front of the list so that it is used as the default installation location for new packages in the current session.

Usage

lib_paths(path, make_path = TRUE, ask = TRUE)

Arguments

Value

A character vector of the folders on the library search path. If path was not omitted, it will be the first element.

Examples

lib_paths()

#> [1] "D:/R/R-3.5.2/library"

lib_paths(file.path(tempdir(), "newlibraryfolder"), ask = FALSE)

#> [1] "C:/Users/.../Temp/Rtmp0Qbvgo/newlibraryfolder"
#> [2] "D:/R/R-3.5.2/library"

Set packages and library paths to automatically start-up with R

Description

This function tells R to load packages and library folders at the start of every session (or on a per-project basis). It's best to keep this auto-load list to a minimum so that you don't forget to explicitly install/attach packages in scripts that need them.

Usage

lib_startup(..., lib = lib_paths(), global = TRUE)

Arguments

Details

R's startup order is mentioned in ?Startup, but briefly:

1. R tries to load the environmental variables file (Renviron.site)

2. R tries to load the site-wide profile (Rprofile.site)

3. R tries to load the user profile (.Rprofile), first in the current directory, and then in the user's home directory (on Windows, the My Documents folder). Only one of these files is sourced into the workspace.

Omitting ... makes R load only its default packages. If these are not set in an environmental variable (R_DEFAULT_PACKAGES), then R will default to loading these packages: datasets, utils, grDevices, graphics, stats, and methods.

Value

A message listing the values that were written to the .Rprofile file.

Examples

#> lib_startup(librarian, magrittr, lib = "C:/Dropbox/My R Library")

List the dependencies of selected packages

Description

List the dependencies of selected packages

Usage

list_dependencies(of_pkgs, which = c("Depends", "Imports"))

Arguments

Value

A character vector of package names. Note that all dependencies of all requested packages will be placed into the one vector.

Build a path, creating subfolders if needed

Description

Whereas base::file.path() only concatenates strings to build a path, make_dirs() also makes sure those folders exist.

Usage

make_dirs(...)

Arguments

Value

(Character) A file path. Automatically adds trailing slashes if required.

Authors

• Desi Quintans (http://www.desiquintans.com)

Source

• Desiderata package (https://github.com/DesiQuintans/desiderata)

Examples

## Not run: 
make_dirs(tempdir(), "newfolder")

#> [1] "C:/Users/.../Temp/RtmpSwZA8X/newfolder"

## End(Not run)

Convert dots to package names

Description

Convert dots to package names

Usage

nse_dots(..., keep_user = FALSE)

Arguments

Value

A character vector.

Examples

## Not run: 
nse_dots(dplyr, DesiQuintans/desiderata, keep_user = FALSE)

#> [1] "dplyr"   "desiderata"

nse_dots(dplyr, DesiQuintans/desiderata, keep_user = TRUE)

#> [1] "dplyr"   "DesiQuintans/desiderata"

## End(Not run)

Detach and then reattach packages to the search path

Description

Convenience shortcut for force-unshelfing packages and then shelfing them again.

Usage

reshelf(...)

Arguments

Value

Invisibly returns a named logical vector, where the names are the packages requested in ... and TRUE means that the package was successfully attached.

Examples

reshelf(datasets)

# reshelf() returns invisibly; bind its output to a variable or access the .Last.value.

print(.Last.value)

#> datasets 
#>     TRUE

Keep the first sentence of a string.

Description

Keep the first sentence of a string.

Usage

sentence(string)

Arguments

Value

The string with only the first sentence.

Examples

## Not run: 
sentence("This is a sentence. And this is another sentence.")

#> [1] "This is a sentence."

sentence("This is just one sentence.")

#> [1] "This is just one sentence."

sentence("Is this a sentence? Or is this one. Maybe this one! What if there are lots of sentences?")

#> [1] "Is this a sentence?

## End(Not run)

Attach packages to the search path, installing them from CRAN, GitHub, or Bioconductor if needed

Description

Attach packages to the search path, installing them from CRAN, GitHub, or Bioconductor if needed

Usage

shelf(
  ...,
  lib = NULL,
  update_all = FALSE,
  quiet = FALSE,
  ask = TRUE,
  cran_repo = getOption("repos"),
  bioc_repo = character()
)

Arguments

Details

You may choose to organise your library into folders to hold packages for different tasks or projects. If you specify a lib folder, it will be created (if needed) and attached to the package search path. R will look for packages by working through the package search path in order. You can view the folders that are on this path by calling lib_paths() with no arguments.

If you specify a new lib and use the argument update_all = TRUE to force an already-installed package to reinstall, a new copy of that package will be made in lib and then loaded from there. This means that you can potentially have several copies of the same package across many folders on your machine, each a different version. This allows you to maintain a different library folder for different projects, so that updated packages in Project B will not affect the package versions you rely on for Project A.

Value

Invisibly returns a named logical vector, where the names are the packages requested in ... and TRUE means that the package was successfully installed and attached.

Examples

shelf(fortunes, DesiQuintans/emptyRpackage, cowsay, lib = tempdir(), update_all = TRUE)

# shelf() returns invisibly; bind its output to a variable or access the .Last.value.

print(.Last.value)

#> fortunes emptyRpackage        cowsay 
#>     TRUE          TRUE          TRUE 

Suppresses console output, including printing

Description

This is copied from my personal package, desiderata.

Usage

shhh(expr)

Arguments

Value

Evaluates expr.

Install packages from CRAN, GitHub, or Bioconductor if needed/wanted

Description

Install packages from CRAN, GitHub, or Bioconductor if needed/wanted

Usage

stock(
  ...,
  lib = NULL,
  update_all = FALSE,
  quiet = FALSE,
  ask = TRUE,
  cran_repo = getOption("repos"),
  bioc_repo = character()
)

Arguments

Details

You may choose to organise your library into folders to hold packages for different tasks or projects. If you specify a lib folder, it will be created (if needed) and attached to the package search path. R will look for packages by working through the package search path in order. You can view the folders that are on this path by calling lib_paths() with no arguments.

If you specify a new lib and use the argument update_all = TRUE to force an already-installed package to reinstall, a new copy of that package will be made in lib and then loaded from there. This means that you can potentially have several copies of the same package across many folders on your machine, each a different version. This allows you to maintain a different library folder for different projects, so that updated packages in Project B will not affect the package versions you rely on for Project A.

Value

Invisibly returns a named logical vector, where the names are the packages requested in ... and TRUE means that the package was successfully installed.

Examples

stock(fortunes, DesiQuintans/emptyRpackage, cowsay, lib = tempdir(), update_all = TRUE)

# shelf() returns invisibly; bind its output to a variable or access the .Last.value.

print(.Last.value)

#> fortunes emptyRpackage        cowsay 
#>     TRUE          TRUE          TRUE 

# And to confirm that they are installed but not attached:

check_attached(fortunes, DesiQuintans/emptyRpackage, cowsay)

#> fortunes emptyRpackage        cowsay 
#>    FALSE         FALSE         FALSE 

Messages for the user

Description

Messages for the user

Usage

tell_user(message, ...)

Arguments

Value

A string.

Examples

## Not run: 
message(tell_user("not allowed to make path", "C:/fakefolder"))

## End(Not run)

Detach (unload) packages from the search path

Description

Packages can be detached by themselves, with their dependencies safely (i.e. as long as those dependencies are not being used by other packages), or with their dependencies unsafely (regardless of whether those dependencies are still needed). All non-default packages can be detached at once too, including Librarian itself.

Usage

unshelf(
  ...,
  everything = FALSE,
  also_depends = FALSE,
  safe = TRUE,
  quiet = TRUE
)

Arguments

Value

Invisibly returns a named logical vector, where the names are the packages and TRUE means that the package was successfully detached.

Examples

# These are the same:

#> unshelf(janitor, desiderata, purrr)
#> unshelf(janitor, DesiQuintans/desiderata, purrr)

# unshelf() returns invisibly; bind its output to a variable or access the .Last.value.

#> print(.Last.value)

#> desiderata    janitor      purrr 
#>       TRUE       TRUE       TRUE 

#> unshelf(everything = TRUE)
#> print(.Last.value)

#> librarian testthat
#> TRUE      TRUE

Produce a nicely-wrapped paragraph for console printing

Description

Wrapping text needs to be done separately from actually printing it with stop or warning or message. This is because these functions typically also print some information about the environment where they were called.

Usage

wrap_text(...)

Arguments

Value

The text in ... will be collapsed and wrapped.

Examples

## Not run: 
wrapped <- 
wrap_text(
    "Lorem ipsum dolor sit amet, ornare justo condimentum",
    "et sit lorem! Himenaeos, vel et sodales sit.",
    "Eu nulla. Magna ullamcorper nascetur placerat platea.\n\n",
    "Eleifend semper velit sed aliquam, ut ligula non commodo.")

cat(wrapped)

#>  Lorem ipsum dolor sit amet, ornare justo condimentum et sit lorem! 
#>  Himenaeos, vel et sodales sit. Eu nulla. Magna ullamcorper 
#>  nascetur placerat platea. 
#>
#>  Eleifend semper velit sed aliquam, ut ligula non commodo.

## End(Not run)