Package 'toscutil'

Title:	Utility Functions
Description:	Base R sometimes requires verbose statements for simple, often recurring tasks, such as printing text without trailing space, ending with newline. This package aims at providing shorthands for such tasks.
Authors:	Tobias Schmidt [aut, cre]
Maintainer:	Tobias Schmidt <[email protected]>
License:	MIT + file LICENSE
Version:	2.8.0
Built:	2024-11-08 04:58:51 UTC
Source:	https://github.com/toscm/toscutil

Help Index

Get Name of Calling Function
Capture output from a command
Concatenate and Print
Concatenate and Print
Concatenate and Print
Format and Print
Format and Print
Concatenate and Print
Concatenate and Print
Concatenate and Print
Check Documented Functions in a Package
Get Normalized Configuration Directory Path of a Program
Get Normalized Configuration File Path of a Program
Return Corners of Matrix like Objects
Get Normalized Data Directory Path of a Program
Docstring Template
Return ASCII representation of an R object
Foreground Color Codes
Find DESCRIPTION File
Get Function Environment as List
Get docstring for a Function
Get formals of a Function
Get Documented Functions in a Package
Get File Directory
Get Project Directory
Return help for topic
Get USERPROFILE or HOME
Shortcut for multiple if else statements
Truth checking as in Python
Get specified Environment as List
Create automatically named List
Return Normalized Path
Get Current Date and Time as String
Return Default if None
Predict Method for Numeric Vectors
Read DESCRIPTION File into a List
Remove all objects from global environment
Split a docstring into a Head, Param and Tail Part
Stub Function Arguments
Terminate a non-interactive R Session
Traces function calls from a package
Untraces function calls from a package
Update docstring for a Function
Get XDG_CONFIG_HOME
Get XDG_DATA_HOME

Get Name of Calling Function

Description

Returns the name of a calling function as string, i.e. if function g calls function f and function f calls caller(2), then string "g" is returned.

Usage

caller(n = 1)
caller(n = 1)

Arguments

`n`	How many frames to go up in the call stack

Details

Be careful when using caller(n) as input to other functions. Due to R's non-standard-evaluation (NES) mechanism it is possible that the function is not executed directly by that function but instead passed on to other functions, i.e. the correct number of frames to go up cannot be predicted a priori. Solutions are to evaluate the function first, store the result in a variable and then pass the variable to the function or to just try out the required number of frames to go up in an interactive session. For further examples see section Examples.

Value

Name of the calling function

Examples

# Here we want to return a list of all variables created inside a function
f <- function(a = 1, b = 2) {
    x <- 3
    y <- 4
    return(locals(without = formalArgs(caller(4))))
    # We need to go 4 frames up, to catch the formalArgs of `f`, because the
    # `caller(4)` argument is not evaluated directly be `formalArgs`.
}
f() # returns either list(x = 3, y = 4) or list(y = 4, x = 3)

# The same result could have been achieved as follows
g <- function(a = 1, b = 2) {
    x <- 3
    y <- 4
    func <- caller(1)
    return(locals(without = c("func", formalArgs(func))))
}
g() # returns either list(x = 3, y = 4) or list(y = 4, x = 3)
# Here we want to return a list of all variables created inside a function
f <- function(a = 1, b = 2) {
    x <- 3
    y <- 4
    return(locals(without = formalArgs(caller(4))))
    # We need to go 4 frames up, to catch the formalArgs of `f`, because the
    # `caller(4)` argument is not evaluated directly be `formalArgs`.
}
f() # returns either list(x = 3, y = 4) or list(y = 4, x = 3)

# The same result could have been achieved as follows
g <- function(a = 1, b = 2) {
    x <- 3
    y <- 4
    func <- caller(1)
    return(locals(without = c("func", formalArgs(func))))
}
g() # returns either list(x = 3, y = 4) or list(y = 4, x = 3)

Capture output from a command

Description

Like classic capture.output(), but with additional arguments collapse and trim.

Usage

capture.output2(..., collapse = "\n", trim = FALSE)
capture.output2(..., collapse = "\n", trim = FALSE)

Arguments

`...`	Arguments passed on to `capture.output()`.
`collapse`	If `TRUE`, lines are collapsed into a single string. If `FALSE`, lines are returned as is. If any character, lines are collapsed using that character.
`trim`	If `TRUE`, leading and trailing whitespace from each line is removed before the lines are collapsed and/or returned.

Value

If collapse is TRUE or "\n", a character vector of length 1. Else, a character vector of length n, where n corresponds to the number of lines outputted by the expression passed to capture.output().

Examples

x <- capture.output2(str(list(a = 1, b = 2, c = 1:3)))
cat2(x)
x <- capture.output2(str(list(a = 1, b = 2, c = 1:3)))
cat2(x)

Concatenate and Print

Description

Same as cat but with an additional argument end, which gets printed after all other elements. Inspired by pythons print command.

Warning: this function is deprecated and should no longer be used. The function is guaranteed to be available as part of the package until the end of 2023 but might removed at any time after 31.12.2023.

Usage

cat0(..., sep = "", end = "")
cat0(..., sep = "", end = "")

Arguments

`...`	objects passed on to cat
`sep`	a character vector of strings to append after each element
`end`	a string to print after all other elements

Value

No return value, called for side effects

Examples

cat0("hello", "world") # prints "helloworld" (without newline)
cat0("hello", "world") # prints "helloworld" (without newline)

Concatenate and Print

Description

Same as cat but with an additional argument end, which gets printed after all other elements. Inspired by pythons print command.

Usage

cat0n(..., sep = "", end = "\n")
cat0n(..., sep = "", end = "\n")

Arguments

`...`	objects passed on to cat
`sep`	a character vector of strings to append after each element
`end`	a string to print after all other elements

Value

No return value, called for side effects

Examples

cat0n("hello", "world") # prints "helloworld\n"
cat0n("hello", "world") # prints "helloworld\n"

Concatenate and Print

Description

Same as base::cat() but with an additional argument end, which gets printed after all other elements. Inspired by pythons print command.

Usage

cat2(
  ...,
  sep = " ",
  end = "\n",
  file = "",
  append = FALSE,
  fill = FALSE,
  labels = NULL
)
cat2(
  ...,
  sep = " ",
  end = "\n",
  file = "",
  append = FALSE,
  fill = FALSE,
  labels = NULL
)

Arguments

`...`	R objects (see 'Details' for the types of objects allowed).
`sep`	a character vector of strings to append after each element.
`end`	a string to print after all other elements.
`file`	A connection, or a character string naming the file to print to. If `""` (the default), `cat2` prints to the standard output connection, the console unless redirected by sink.
`append`	logical. Only used if the argument `file` is the name of file (and not a connection or `"\|cmd"`). If `TRUE` output will be appended to `file`; otherwise, it will overwrite the contents of `file`.
`fill`	a logical or (positive) numeric controlling how the output is broken into successive lines. If `FALSE` (default), only newlines created explicitly by `"\n"` are printed. Otherwise, the output is broken into lines with print width equal to the option `width` if `fill` is `TRUE`, or the value of `fill` if this is numeric. Linefeeds are only inserted between elements, strings wider than `fill` are not wrapped. Non-positive `fill` values are ignored, with a warning.
`labels`	character vector of labels for the lines printed. Ignored if `fill` is `FALSE`.

Value

No return value, called for side effects

Examples

x <- 1
cat("x:", x, "\n") # prints 'Number: 1 \n' (with a space between 1 and \n)
cat2("x:", x) # prints 'Number: 1\n'  (without space)
x <- 1
cat("x:", x, "\n") # prints 'Number: 1 \n' (with a space between 1 and \n)
cat2("x:", x) # prints 'Number: 1\n'  (without space)

Format and Print

Description

Same as cat(sprintf(fmt, ...))

Usage

catf(fmt, ..., file = "", append = FALSE, fill = FALSE, labels = NULL)
catf(fmt, ..., file = "", append = FALSE, fill = FALSE, labels = NULL)

Arguments

`fmt`	A character vector of format strings, each of up to 8192 bytes.
`...`	Up to 100 values to be passed into `fmt`. Only logical, integer, real and character vectors are supported, but some coercion will be done: see the Details section of `base::sprintf()`.
`file`	A connection, or a character string naming the file to print to. If `""` (the default), `cat2` prints to the standard output connection, the console unless redirected by sink.
`append`	logical. Only used if the argument `file` is the name of file (and not a connection or `"\|cmd"`). If `TRUE` output will be appended to `file`; otherwise, it will overwrite the contents of `file`.
`fill`	a logical or (positive) numeric controlling how the output is broken into successive lines. If `FALSE` (default), only newlines created explicitly by `"\n"` are printed. Otherwise, the output is broken into lines with print width equal to the option `width` if `fill` is `TRUE`, or the value of `fill` if this is numeric. Linefeeds are only inserted between elements, strings wider than `fill` are not wrapped. Non-positive `fill` values are ignored, with a warning.
`labels`	character vector of labels for the lines printed. Ignored if `fill` is `FALSE`.

Value

No return value, called for side effects

Examples

catf("A%dB%sC", 2, "asdf") # prints "A2BasdfC"
catf("A%dB%sC", 2, "asdf") # prints "A2BasdfC"

Format and Print

Description

Same as cat2(sprintf(fmt, ...))

Usage

catfn(
  fmt,
  ...,
  end = "\n",
  file = "",
  sep = " ",
  fill = FALSE,
  labels = NULL,
  append = FALSE
)
catfn(
  fmt,
  ...,
  end = "\n",
  file = "",
  sep = " ",
  fill = FALSE,
  labels = NULL,
  append = FALSE
)

Arguments

`fmt`	passed on to `base::sprintf()`
`...`	passed on to `base::sprintf()`
`end`	passed on to `cat2()`
`file`	passed on to `cat2()` (which passes it on to `base::cat()`)
`sep`	passed on to `cat2()` (which passes it on to `base::cat()`)
`fill`	passed on to `cat2()` (which passes it on to `base::cat()`)
`labels`	passed on to `cat2()` (which passes it on to `base::cat()`)
`append`	passed on to `cat2()` (which passes it on to `base::cat()`)

Value

No return value, called for side effects

Examples

catfn("A%dB%sC", 2, "asdf") # prints "A2BasdfC\n"
catfn("A%dB%sC", 2, "asdf") # prints "A2BasdfC\n"

Concatenate and Print

Description

Same as cat but with an additional argument end, which gets printed after all other elements. Inspired by pythons print command.

Usage

catn(..., sep = " ", end = "\n")
catn(..., sep = " ", end = "\n")

Arguments

`...`	objects passed on to cat
`sep`	a character vector of strings to append after each element
`end`	a string to print after all other elements

Value

No return value, called for side effects

Examples

catn("hello", "world") # prints "hello world\n"
catn("hello", "world") # prints "hello world\n"

Concatenate and Print

Description

Same as cat but with an additional argument end, which gets printed after all other elements. Inspired by pythons print command.

Usage

catnn(..., sep = "\n", end = "\n")
catnn(..., sep = "\n", end = "\n")

Arguments

`...`	objects passed on to cat
`sep`	a character vector of strings to append after each element
`end`	a string to print after all other elements

Value

No return value, called for side effects

Examples

catnn("hello", "world") # prints "hello\nworld\n"
catnn("hello", "world") # prints "hello\nworld\n"

Concatenate and Print

Description

Same as cat but with an additional argument end, which gets printed after all other elements. Inspired by pythons print command.

Usage

catsn(..., sep = " ", end = "\n")
catsn(..., sep = " ", end = "\n")

Arguments

`...`	objects passed on to cat
`sep`	a character vector of strings to append after each element
`end`	a string to print after all other elements

Value

No return value, called for side effects

Examples

catsn("hello", "world") # prints "hello world\n"
catsn("hello", "world") # prints "hello world\n"

Check Documented Functions in a Package

Description

Lists all documented functions in a package and checks their documentation elements for potential issues. The following checks are performed:

Title is present and doesn't start with regex "Function".
Description is present and doesn't start with "This function".
Value is present.
Example is present.

Usage

check_pkg_docs(pkg = NULL)
check_pkg_docs(pkg = NULL)

Arguments

pkg

The package name. If NULL, the package name is inferred from the DESCRIPTION file in the current directory or any parent directory. If no DESCRIPTION file is found, the function stops with an error message.

Value

Returns a dataframe with columns title, description, value, examples and rows corresponding to the documented functions in the package. Each cell contains a string describing the check result for the corresponding documentation element of that function.

Examples

df <- check_pkg_docs("tools")
try(df <- check_pkg_docs())
df <- check_pkg_docs("tools")
try(df <- check_pkg_docs())

Get Normalized Configuration Directory Path of a Program

Description

config_dir returns the absolute, normalized path to the configuration directory of a program/package/app based on an optional app-specific commandline argument, an optional app-specific environment variable and the XDG Base Directory Specification

Usage

config_dir(
  app_name,
  cl_arg = commandArgs()[grep("--config-dir", commandArgs()) + 1],
  env_var = Sys.getenv(toupper(paste0(app_name, "_config_dir()"))),
  create = FALSE,
  sep = "/"
)
config_dir(
  app_name,
  cl_arg = commandArgs()[grep("--config-dir", commandArgs()) + 1],
  env_var = Sys.getenv(toupper(paste0(app_name, "_config_dir()"))),
  create = FALSE,
  sep = "/"
)

Arguments

`app_name`	Name of the program/package/app
`cl_arg`	Value of app specific commandline parameter
`env_var`	Value of app specific environment variable
`create`	whether to create returned path, if it doesn't exists yet
`sep`	Path separator to be used on Windows

Details

The following algorithm is used to determine the location of the configuration directory for application ⁠$app_name⁠:

If parameter cl_arg is a non-empty string, return it
Else, if parameter env_var is a non-empty string, return it
Else, if environment variable (EV) XDG_CONFIG_HOME exists, return ⁠$XDG_CONFIG_HOME/$app_name⁠
Else, if EV HOME exists, return ⁠$HOME/.config/{app_name}⁠
Else, if EV USERPROFILE exists, return ⁠$USERPROFILE/.config/{app_name}⁠
Else, return ⁠$WD/.config/{app-name}⁠

where ⁠$WD⁠ equals the current working directory and the notation ⁠$VAR⁠ is used to specify the value of a parameter or environment variable VAR.

Value

Normalized path to the configuration directory of ⁠$app_name⁠.

Examples

config_dir("myApp")
config_dir("myApp")

Get Normalized Configuration File Path of a Program

Description

config_file returns the absolute, normalized path to the configuration file of a program/package/app based on an optional app-specific commandline argument, an optional app-specific environment variable and the XDG Base Directory Specification

Usage

config_file(
  app_name,
  file_name,
  cl_arg = commandArgs()[grep("--config-file", commandArgs()) + 1],
  env_var = "",
  sep = "/",
  copy_dir = norm_path(xdg_config_home(), app_name),
  fallback_path = NULL
)
config_file(
  app_name,
  file_name,
  cl_arg = commandArgs()[grep("--config-file", commandArgs()) + 1],
  env_var = "",
  sep = "/",
  copy_dir = norm_path(xdg_config_home(), app_name),
  fallback_path = NULL
)

Arguments

`app_name`	Name of the program/package/app
`file_name`	Name of the configuration file
`cl_arg`	Value of app specific commandline parameter
`env_var`	Value of app specific environment variable
`sep`	Path separator to be used on Windows
`copy_dir`	Path to directory where `⁠$fallback_path⁠` should be copied to in case it gets used.
`fallback_path`	Value to return as fallback (see details)

Details

The following algorithm is used to determine the location of ⁠$file_name⁠:

If ⁠$cl_arg⁠ is a non-empty string, return it
Else, if ⁠$env_var⁠ is a non-empty string, return it
Else, if ⁠$PWD/.config/$app_name⁠ exists, return it
Else, if ⁠$XDG_CONFIG_HOME/$app_name/$file_name⁠ exists, return it
Else, if ⁠$HOME/.config/$app_name/$file_name⁠ exists, return it
Else, if ⁠$USERPROFILE/.config/$app_name/$file_name⁠ exists, return it
Else, if ⁠$copy_dir⁠ is non-empty string and ⁠$fallback_path⁠ is a path to an existing file, then try to copy ⁠$fallback_path⁠ to copy_dir/⁠$file_name⁠ and return copy_dir/⁠$file_name⁠ (Note, that in case $copy_dir is a non-valid path, the function will throw an error.)
Else, return $fallback_path

Value

Normalized path to the configuration file of ⁠$app_name⁠.

Examples

config_dir("myApp")
config_dir("myApp")

Return Corners of Matrix like Objects

Description

Similar to head() and tail(), but returns n rows/cols from each side of x (i.e. the corners of x).

Usage

corn(x, n = 2L)
corn(x, n = 2L)

Arguments

`x`	matrix like object
`n`	number of cols/rows from each corner to return

Value

x[c(1:n, N-n:N), c(1:n, N-n:N)]

Examples

corn(matrix(1:10000, 100))
corn(matrix(1:10000, 100))

Get Normalized Data Directory Path of a Program

Description

data_dir returns the absolute, normalized path to the data directory of a program/package/app based on an optional app-specific commandline argument, an optional app-specific environment variable and the XDG Base Directory Specification

Usage

data_dir(
  app_name,
  cl_arg = commandArgs()[grep("--data-dir", commandArgs()) + 1],
  env_var = Sys.getenv(toupper(paste0(app_name, "_DATA_DIR"))),
  create = FALSE,
  sep = "/"
)
data_dir(
  app_name,
  cl_arg = commandArgs()[grep("--data-dir", commandArgs()) + 1],
  env_var = Sys.getenv(toupper(paste0(app_name, "_DATA_DIR"))),
  create = FALSE,
  sep = "/"
)

Arguments

`app_name`	Name of the program/package/app
`cl_arg`	Value of app specific commandline parameter
`env_var`	Value of app specific environment variable
`create`	whether to create returned path, if it doesn't exists yet
`sep`	Path separator to be used on Windows

Details

The following algorithm is used to determine the location of the data directory for application ⁠$app_name⁠:

If parameter ⁠$cl_arg⁠ is a non-empty string, return cl_arg
Else, if parameter ⁠$env_var⁠ is a non-empty string, return ⁠$env_var⁠
Else, if environment variable (EV) ⁠$XDG_DATA_HOME⁠ exists, return ⁠$XDG_DATA_HOME/$app_name⁠
Else, if EV ⁠$HOME⁠ exists, return ⁠$HOME/.local/share/$app_name⁠
Else, if EV ⁠$USERPROFILE⁠ exists, return ⁠$USERPROFILE/.local/share/$app_name⁠
Else, return ⁠$WD/.local/share⁠

Value

Normalized path to the data directory of ⁠$app_name⁠.

Examples

data_dir("myApp")
data_dir("myApp")

Docstring Template

Description

A minimal docstring template

Usage

DOCSTRING_TEMPLATE
DOCSTRING_TEMPLATE

Format

A single string, i.e. a character vector of length 1.

Examples

cat(DOCSTRING_TEMPLATE)
cat(DOCSTRING_TEMPLATE)

Return ASCII representation of an R object

Description

Like classic dput(), but instead of writing to stdout, the text representation is returned as string.

Usage

dput2(..., collapse = " ", trim = TRUE)
dput2(..., collapse = " ", trim = TRUE)

Arguments

`...`	Arguments passed on to `dput()`.
`collapse`	Character to use for collapsing the lines.
`trim`	If `TRUE`, leading and trailing whitespace from each line is cleared before the lines are collapsed and/or returned.

Value

If collapse == '\n', a character vector of length 1. Else, a character vector of length n, where n corresponds to the number of lines outputted by classic dput().

Examples

# Classic dput prints directly to stdout
x <- iris[1, ]
dput(x)

# Traditional formatting using dput2
y <- dput2(x, collapse = "\n", trim = FALSE)
cat2(y)

# Single line formatting
z <- dput2(x)
cat2(z)
# Classic dput prints directly to stdout
x <- iris[1, ]
dput(x)

# Traditional formatting using dput2
y <- dput2(x, collapse = "\n", trim = FALSE)
cat2(y)

# Single line formatting
z <- dput2(x)
cat2(z)

Foreground Color Codes

Description

Provides ANSI escape codes as a named list for changing terminal text colors and style resetting. These codes can modify the foreground color and reset styles to defaults (incl. background color and text formatting).

Usage

fg
fg

Format

A named list of ANSI escape codes for text coloring and style resetting in the terminal. Includes colors: GREY, RED, GREEN, YELLOW, BLUE, PURPLE, CYAN, WHITE, and RESET for default style restoration.

Examples

cat(fg$RED, "This text will be red.", fg$RESET, "\n")
cat(fg$GREEN, "This text will be green.", fg$RESET, "\n")
cat(fg$RESET, "Text back to default.", "\n")
cat(fg$RED, "This text will be red.", fg$RESET, "\n")
cat(fg$GREEN, "This text will be green.", fg$RESET, "\n")
cat(fg$RESET, "Text back to default.", "\n")

Find DESCRIPTION File

Description

Searches for a DESCRIPTION file starting from the current or specified directory and moving upwards through the directory hierarchy until the file is found or the root directory is reached.

Usage

find_description_file(start_dir = getwd())
find_description_file(start_dir = getwd())

Arguments

start_dir

The starting directory for the search. Defaults to the current working directory.

Value

The path to the DESCRIPTION file if found. If not found, the function stops with an error message.

Examples

# Start search from a specific directory
graphics_pkg_dir <- system.file(package = "graphics")
find_description_file(graphics_pkg_dir)

## Not run: 
# Below example will only work if executed from a package directory
find_description_file()

## End(Not run)
# Start search from a specific directory
graphics_pkg_dir <- system.file(package = "graphics")
find_description_file(graphics_pkg_dir)

## Not run: 
# Below example will only work if executed from a package directory
find_description_file()

## End(Not run)

Get Function Environment as List

Description

Returns the function environment as list. Raises an error when called outside a function. By default, objects specified as arguments are removed from the environment.

Usage

function_locals(without = c(), strip_function_args = TRUE)
function_locals(without = c(), strip_function_args = TRUE)

Arguments

`without`	character vector of symbols to exclude
`strip_function_args`	Whether to exclude symbols with the same name as the function arguments

Details

The order of the symbols in the returned list is arbitrary.

Value

The function environment as list

Examples

f <- function(a = 1, b = 2) {
    x <- 3
    y <- 4
    return(function_locals())
}
all.equal(setdiff(f(), list(x = 3, y = 4)), list())
f <- function(a = 1, b = 2) {
    x <- 3
    y <- 4
    return(function_locals())
}
all.equal(setdiff(f(), list(x = 3, y = 4)), list())

Get docstring for a Function

Description

The roxygen2 package makes it possible to write documentation for R functions directly above the corresponding function. This function can be used to retrieve the full documentation string (docstring).

Usage

get_docstring(content, func, collapse = TRUE, template = DOCSTRING_TEMPLATE)
get_docstring(content, func, collapse = TRUE, template = DOCSTRING_TEMPLATE)

Arguments

`content`	R code as string.
`func`	Name of function to get docstring for.
`collapse`	Whether to collapse all docstring into a single string.
`template`	String to return in case no docstring could be found.

Value

A character vector of length 1 containing either the docstring or the empty string (in case no documentation could be detected).

Examples

uri <- system.file("testfiles/funcs.R", package = "toscutil")
content <- readLines(uri)
func <- "f2"
get_docstring(content, func)
get_docstring(content, func, collapse = TRUE)
uri <- system.file("testfiles/funcs.R", package = "toscutil")
content <- readLines(uri)
func <- "f2"
get_docstring(content, func)
get_docstring(content, func, collapse = TRUE)

Get formals of a Function

Description

Returns the arguments of a function from a valid R file.

Usage

get_formals(uri, content, func)
get_formals(uri, content, func)

Arguments

`uri`	Path to R file.
`content`	R code as string.
`func`	Function name. If a function is defined multiple times inside the provided file, only the last occurence will be considered.

Value

A named character vector as returned by formals().

Examples

uri <- system.file("testfiles/funcs.R", package = "toscutil")
content <- readLines(uri)
func <- "f2"
if (requireNamespace("languageserver", quietly = TRUE)) {
    get_formals(uri, content, func)
}
uri <- system.file("testfiles/funcs.R", package = "toscutil")
content <- readLines(uri)
func <- "f2"
if (requireNamespace("languageserver", quietly = TRUE)) {
    get_formals(uri, content, func)
}

Get Documented Functions in a Package

Description

Lists all documented functions in a package together with some of their documentation elements as raw text. Only works for installed packages.

Usage

get_pkg_docs(pkg = NULL, unload = TRUE, reload = TRUE)
get_pkg_docs(pkg = NULL, unload = TRUE, reload = TRUE)

Arguments

`pkg`	The package name. If NULL, the package name is inferred from the DESCRIPTION file in the current directory or any parent directory. If no DESCRIPTION file is found, the function stops with an error message.
`unload`	Whether to unload a potential currently developed package using `devtools::unload()` before checking the documentation. Required when the package was loaded with `devtools::load_all()` as the documentation database only exists for installed packages.
`reload`	Whether to reload the package using `devtools::load_all()` after checking the documentation.

Value

Returns a dataframe with columns title, description, value, examples and rows corresponding to the documented functions in the package.

Examples

df <- get_pkg_docs("tools")
nchars <- as.data.frame(apply(df, 2, function(col) sapply(col, nchar)))
head(nchars)
df <- get_pkg_docs("tools")
nchars <- as.data.frame(apply(df, 2, function(col) sapply(col, nchar)))
head(nchars)

Get File Directory

Description

Return full path to current file directory

Usage

getfd(
  on.error = stop("No file sourced. Maybe you're in an interactive shell?", call. =
    FALSE),
  winslash = "/"
)
getfd(
  on.error = stop("No file sourced. Maybe you're in an interactive shell?", call. =
    FALSE),
  winslash = "/"
)

Arguments

`on.error`	Expression to use if the current file directory cannot be determined. In that case, `normalizePath(on.error, winslash)` is returned. Can also be an expression like `stop("message")` to stop execution (default).
`winslash`	Path separator to use for windows

Value

Current file directory as string

Examples

getfd(on.error = getwd())
## Not run: 
getfd()

## End(Not run)
getfd(on.error = getwd())
## Not run: 
getfd()

## End(Not run)

Get Project Directory

Description

Find the project root directory by traversing the current working directory filepath upwards until a given set of files is found.

Usage

getpd(root.files = c(".git", "DESCRIPTION", "NAMESPACE"))
getpd(root.files = c(".git", "DESCRIPTION", "NAMESPACE"))

Arguments

root.files

if any of these files is found in a parent folder, the path to that folder is returned

Value

getpd returns the absolute, normalized project root directory as string. The forward slash is used as path separator (independent of the OS).

Examples

local({
     base_pkg_root_dir <- system.file(package = "base")
     base_pkg_R_dir <- file.path(base_pkg_root_dir, "R")
     owd <- setwd(base_pkg_R_dir); on.exit(setwd(owd))
     getpd()
})
local({
     base_pkg_root_dir <- system.file(package = "base")
     base_pkg_R_dir <- file.path(base_pkg_root_dir, "R")
     owd <- setwd(base_pkg_R_dir); on.exit(setwd(owd))
     getpd()
})

Return help for topic

Description

Returns the help text for the specified topic formatted either as plain text, html or latex.

Usage

help2(topic, format = "text", package = NULL)
help2(topic, format = "text", package = NULL)

Arguments

`topic`	character, the topic for which to return the help text. See argument `topic` of function `help()` for details.
`format`	character, either `"text"`, `"html"` or `"latex"`
`package`	character, the package for which to return the help text. This argument will be ignored if topic is specified. Package must be attached to the search list first, e.g. by calling `library(package)`.

Value

The help text for the specified topic in the specified format as string.

Examples

htm <- help2("sum", "html")
txt <- help2(topic = "sum", format = "text")
cat2(txt)
htm <- help2("sum", "html")
txt <- help2(topic = "sum", format = "text")
cat2(txt)

Get USERPROFILE or HOME

Description

Returns normalized value of environment variable USERPROFILE, if defined, else value of HOME.

Usage

home(winslash = "/")
home(winslash = "/")

Arguments

winslash

path separator to be used on Windows (passed on to normalizePath)

Value

normalized value of environment variable USERPROFILE, if defined, else value of HOME.

Examples

home()
home()

Shortcut for multiple if else statements

Description

ifthen(a, b, c, d, e, f, ...) == if (a) b else if (c) d else if (e) f

Usage

ifthen(...)
ifthen(...)

Arguments

...

pairs of checks and corresponding return values

Value

ifelse returns the first value for which the corresponding statement evaluates to TRUE

Examples

x <- 2
y <- 2
z <- 1
ifthen(x == 0, "foo", y == 0, "bar", z == 1, "this string gets returned")
x <- 2
y <- 2
z <- 1
ifthen(x == 0, "foo", y == 0, "bar", z == 1, "this string gets returned")

Truth checking as in Python

Description

Returns TRUE if x is either FALSE, 0, NULL, NAand empty lists or an empty string. Inspired by python's bool.

Usage

is.none(x)
is.none(x)

Arguments

`x`	object to test

Value

TRUE if x is FALSE, 0, NULL, NA, an empty list or an empty string. Else FALSE.

Examples

is.none(FALSE) # TRUE
is.none(0) # TRUE
is.none(1) # FALSE
is.none(NA) # TRUE
is.none(list()) # TRUE
is.none("") # TRUE
is.none(character()) # TRUE
is.none(numeric()) # TRUE
is.none(logical()) # TRUE
is.none(FALSE) # TRUE
is.none(0) # TRUE
is.none(1) # FALSE
is.none(NA) # TRUE
is.none(list()) # TRUE
is.none("") # TRUE
is.none(character()) # TRUE
is.none(numeric()) # TRUE
is.none(logical()) # TRUE

Get specified Environment as List

Description

Return all symbols in the specified environment as list.

Usage

locals(without = c(), env = parent.frame())
locals(without = c(), env = parent.frame())

Arguments

`without`	Character vector. Symbols from current env to exclude.
`env`	Environment to use. Defaults to the environment from which `locals` is called.

Value

Specified environment as list (without the mentioned symbols).

Examples

f <- function() {
     x <- 1
     y <- 2
     z <- 3
     locals()
}
ret <- f()
stopifnot(identical(ret, list(z = 3, y = 2, x = 1)))
f <- function() {
     x <- 1
     y <- 2
     z <- 3
     locals()
}
ret <- f()
stopifnot(identical(ret, list(z = 3, y = 2, x = 1)))

Create automatically named List

Description

Like normal list(), except that unnamed elements are automatically named according to their symbol

Usage

named(...)
named(...)

Arguments

...

List elements

Value

Object of type list with names attribute set

Examples

a <- 1:10
b <- "helloworld"
l1 <- list(a, b)
names(l1) <- c("a", "b")
l2 <- named(a, b)
stopifnot(identical(l1, l2))
l3 <- list(z = a, b = b)
l4 <- named(z = a, b)
stopifnot(identical(l3, l4))
a <- 1:10
b <- "helloworld"
l1 <- list(a, b)
names(l1) <- c("a", "b")
l2 <- named(a, b)
stopifnot(identical(l1, l2))
l3 <- list(z = a, b = b)
l4 <- named(z = a, b)
stopifnot(identical(l3, l4))

Return Normalized Path

Description

Shortcut for normalizePath(file.path(...), winslash = sep, mustWork = FALSE)

Usage

norm_path(..., sep = "/")
norm_path(..., sep = "/")

Arguments

`...`	Parts used to construct the path
`sep`	Path separator to be used on Windows

Value

Normalized path constructed from ...

Examples

norm_path("C:/Users/max", "a\\b", "c") # returns C:/Users/max/a/b/c
norm_path("a\\b", "c") # return <current-working-dir>/a/b/c
norm_path("C:/Users/max", "a\\b", "c") # returns C:/Users/max/a/b/c
norm_path("a\\b", "c") # return <current-working-dir>/a/b/c

Get Current Date and Time as String

Description

Returns the current system time as a string in the format ⁠YYYY-MM-DD hh:mm:ss[.XX][ TZ]⁠. Square brackets indicate optional parts of the string, 'XX' stands for milliseconds and 'TZ' for 'Timezone'.

Usage

now(usetz = TRUE, color = NULL, digits.sec = 0)

now_ms(usetz = TRUE, color = NULL, digits.sec = 2)
now(usetz = TRUE, color = NULL, digits.sec = 0)

now_ms(usetz = TRUE, color = NULL, digits.sec = 2)

Arguments

`usetz`	Logical, indicating whether to include the timezone in the output.
`color`	Optional color to use for the timestamp. This parameter is only effective if the output is directed to a terminal that supports color, which is checked via `isatty(stdout())`.
`digits.sec`	Integer, the number of digits to include for seconds. Default is 0.

Value

For now, the current system time as a string in the format ⁠YYYY-MM-DD hh:mm:ss TZ⁠. For now_ms, the format is ⁠YYYY-MM-DD hh:mm:ss.XX TZ⁠, where XX represents milliseconds.

Examples

now()                   # "2021-11-27 19:19:31 CEST"
now_ms()                # "2022-06-30 07:14:26.82 CEST"
now(usetz = FALSE)      # "2022-06-30 07:14:26.82"
now(color = fg$GREY)    # "\033[1;30m2024-06-27 14:41:20 CEST\033[0m"
now()                   # "2021-11-27 19:19:31 CEST"
now_ms()                # "2022-06-30 07:14:26.82 CEST"
now(usetz = FALSE)      # "2022-06-30 07:14:26.82"
now(color = fg$GREY)    # "\033[1;30m2024-06-27 14:41:20 CEST\033[0m"

Return Default if None

Description

Like rlang::%||%() but also checks for empty lists and empty strings.

Usage

x %none% y
x %none% y

Arguments

`x`	object to test
`y`	object to return if `is.none(x)`

Value

Returns y if is.none(x) else x

Examples

FALSE %none% 2 # returns 2
0 %none% 2 # returns 2
NA %none% 2 # returns 2
list() %none% 2 # returns 2
"" %none% 2 # returns 2
1 %none% 2 # returns 1
FALSE %none% 2 # returns 2
0 %none% 2 # returns 2
NA %none% 2 # returns 2
list() %none% 2 # returns 2
"" %none% 2 # returns 2
1 %none% 2 # returns 1

Predict Method for Numeric Vectors

Description

Interprets the provided numeric vector as linear model and uses it to generate predictions. If an element of the numeric vector has the name "Intercept" this element is treated as the intercept of the linear model.

Usage

## S3 method for class 'numeric'
predict(object, newdata, ...)
## S3 method for class 'numeric'
predict(object, newdata, ...)

Arguments

`object`	Named numeric vector of beta values. If an element is named "Intercept", that element is interpreted as model intercept.
`newdata`	Matrix with samples as rows and features as columns.
`...`	further arguments passed to or from other methods

Value

Named numeric vector of predicted scores

Examples

X <- matrix(1:4, 2, 2, dimnames = list(c("s1", "s2"), c("a", "b")))
b <- c(Intercept = 3, a = 2, b = 1)
predict(b, X)
X <- matrix(1:4, 2, 2, dimnames = list(c("s1", "s2"), c("a", "b")))
b <- c(Intercept = 3, a = 2, b = 1)
predict(b, X)

Read DESCRIPTION File into a List

Description

Reads the DESCRIPTION file of an R package and converts it into a list where each element corresponds to a field in the DESCRIPTION file.

Usage

read_description_file(p = NULL)
read_description_file(p = NULL)

Arguments

`p`	The path to the DESCRIPTION file. If `NULL`, the function attempts to find the DESCRIPTION file by searching upwards from the current directory.

Value

A list where each element is a field from the DESCRIPTION file.

Examples

# Read DECRIPTION file from a specific path
graphics_pkg_dir <- system.file(package = "graphics")
graphics_pkg_descfile <- find_description_file(graphics_pkg_dir)
desc_list <- read_description_file(graphics_pkg_descfile)
str(desc_list)

## Not run: 
# Below example will only work if executed from a package directory
read_description_file()

## End(Not run)
# Read DECRIPTION file from a specific path
graphics_pkg_dir <- system.file(package = "graphics")
graphics_pkg_descfile <- find_description_file(graphics_pkg_dir)
desc_list <- read_description_file(graphics_pkg_descfile)
str(desc_list)

## Not run: 
# Below example will only work if executed from a package directory
read_description_file()

## End(Not run)

Remove all objects from global environment

Description

Same as rm(list=ls())

Usage

rm_all()
rm_all()

Value

No return value, called for side effects

Examples

## Not run: rm_all()
## Not run: rm_all()

Split a docstring into a Head, Param and Tail Part

Description

Split a docstring into a head, param and tail part.

Usage

split_docstring(docstring)
split_docstring(docstring)

Arguments

docstring

Docstring of a R function as string, i.e. as character vector of length 1.

Value

List with 3 elements: head, param and tail.

Examples

uri <- system.file("testfiles/funcs.R", package = "toscutil")
func <- "f4"
content <- readLines(uri)
docstring <- get_docstring(content, func)
split_docstring(docstring)
uri <- system.file("testfiles/funcs.R", package = "toscutil")
func <- "f4"
content <- readLines(uri)
docstring <- get_docstring(content, func)
split_docstring(docstring)

Stub Function Arguments

Description

stub() assigns all arguments of a given function as symbols to the specified environment (usually the current environment)

Usage

stub(func, ..., envir = parent.frame())
stub(func, ..., envir = parent.frame())

Arguments

`func`	function for which the arguments should be stubbed
`...`	non-default arguments of `func`
`envir`	environment to which symbols should be assigned

Details

Stub is thought to be used for interactive testing and unit testing. It does not work for primitive functions.

Value

list of symbols that are assigned to envir

Examples

f <- function(x, y = 2, z = 3) x + y + z
args <- stub(f, x = 1) # assigns x = 1, y = 2 and z = 3 to current env
f <- function(x, y = 2, z = 3) x + y + z
args <- stub(f, x = 1) # assigns x = 1, y = 2 and z = 3 to current env

Terminate a non-interactive R Session

Description

Similar to python's sys.exit. If used interactively, code execution is stopped with an error message, giving the provided status code. If used non-interactively (e.g. through Rscript), code execution is stopped silently and the process exits with the provided status code.

Usage

sys.exit(status = 0)
sys.exit(status = 0)

Arguments

status

exitcode for R process

Value

No return value, called for side effects

Examples

## Not run: 
if (!file.exists("some.file")) {
    cat("Error: some.file does not exist.\n", file = stderr())
    sys.exit(1)
} else if (Sys.getenv("IMPORTANT_ENV") == "") {
    cat("Error: IMPORTANT_ENV not set.\n", file = stderr())
    sys.exit(2)
} else {
    cat("Everything good. Starting calculations...")
    # ...
    cat("Finished with success!")
    sys.exit(0)
}

## End(Not run)
## Not run: 
if (!file.exists("some.file")) {
    cat("Error: some.file does not exist.\n", file = stderr())
    sys.exit(1)
} else if (Sys.getenv("IMPORTANT_ENV") == "") {
    cat("Error: IMPORTANT_ENV not set.\n", file = stderr())
    sys.exit(2)
} else {
    cat("Everything good. Starting calculations...")
    # ...
    cat("Finished with success!")
    sys.exit(0)
}

## End(Not run)

Traces function calls from a package

Description

Traces all function calls from a package and writes them to file with timestamps and callstack depth. Should always be used in combination with untrace_package() to untrace the package after use. For example ⁠trace_package("graphics"); on.exit(untrace_package("graphics")⁠. See examples for more details.

Usage

trace_package(
  pkg,
  file = stdout(),
  max = Inf,
  funign = character(),
  opsign = TRUE,
  dotign = TRUE,
  silent = TRUE,
  exitmsg = "exit"
)
trace_package(
  pkg,
  file = stdout(),
  max = Inf,
  funign = character(),
  opsign = TRUE,
  dotign = TRUE,
  silent = TRUE,
  exitmsg = "exit"
)

Arguments

`pkg`	Package name to trace.
`file`	File to write to.
`max`	Maximum depth of callstack to print.
`funign`	Functions to ignore.
`opsign`	Whether to ignore operators.
`dotign`	Whether to ignore functions starting with a dot.
`silent`	Whether to suppress messages.
`exitmsg`	Message to print on function exits.

Details

Some function define their own on.exit() handlers with option add = FALSE. For those functions, exit tracing is impossible (as described in trace()). For now those functions have to be detected and ignored manually by the user using argument funign.

Value

No return value, called for side effects

Examples

## Not run: 
# Trace all function from the graphics package, except for `plot.default`
# as it defines its own on.exit() handler, i.e. exit tracing is impossible.
local({
    trace_package("graphics", funign = "plot.default")
    on.exit(untrace_package("graphics"), add = TRUE)
    plot(1:10)
})

## End(Not run)
## Not run: 
# Trace all function from the graphics package, except for `plot.default`
# as it defines its own on.exit() handler, i.e. exit tracing is impossible.
local({
    trace_package("graphics", funign = "plot.default")
    on.exit(untrace_package("graphics"), add = TRUE)
    plot(1:10)
})

## End(Not run)

Untraces function calls from a package

Description

Removes tracing from all function calls in a package that were previously traced by trace_package().

Usage

untrace_package(pkg)
untrace_package(pkg)

Arguments

pkg

Package name to untrace.

Details

This function reverses the effects of trace_package by removing all tracing from the specified package's functions.

Value

No return value, called for side effects

Examples

## Not run: 
local({
    trace_package("graphics", funign = "plot.default")
    on.exit(untrace_package("graphics"), add = TRUE)
    plot(1:10)
})

## End(Not run)
## Not run: 
local({
    trace_package("graphics", funign = "plot.default")
    on.exit(untrace_package("graphics"), add = TRUE)
    plot(1:10)
})

## End(Not run)

Update docstring for a Function

Description

The roxygen2 package makes it possible to write documentation for R functions directly above the corresponding function. This function can be used to update the parameter list of a documentation string (docstring) of a valid function of a valid R file. The update is done by comparing the currently listed parameters with the actual function parameters. Outdated parameters are removed and missing parameters are added to the docstring.

Usage

update_docstring(uri, func, content = NULL)
update_docstring(uri, func, content = NULL)

Arguments

`uri`	Path to R file.
`func`	Function name. If a function is defined multiple times inside the provided file, only the last occurence will be considered.
`content`	R code as string. If provided, uri is ignored.

Value

A character vector of length 1 containing the updated docstring.

Examples

uri <- system.file("testfiles/funcs.R", package = "toscutil")
func <- "f4"
update_docstring(uri, func)
uri <- system.file("testfiles/funcs.R", package = "toscutil")
func <- "f4"
update_docstring(uri, func)

Get XDG_CONFIG_HOME

Description

Return value for XDG_CONFIG_HOME as defined by the XDG Base Directory Specification

Usage

xdg_config_home(sep = "/", fallback = normalizePath(getwd(), winslash = sep))
xdg_config_home(sep = "/", fallback = normalizePath(getwd(), winslash = sep))

Arguments

`sep`	Path separator to be used on Windows
`fallback`	Value to return as fallback (see details)

Value

The following algorithm is used to determine the returned path:

If environment variable (EV) XDG_CONFIG_HOME exists, return its value
Else, if EV HOME exists, return ⁠$HOME/.config⁠
Else, if EV USERPROFILE exists, return ⁠$USERPROFILE/.config⁠
Else, return ⁠$fallback⁠

Examples

xdg_config_home()
xdg_config_home()

Get XDG_DATA_HOME

Description

Return value for XDG_DATA_HOME as defined by the XDG Base Directory Specification

Usage

xdg_data_home(sep = "/", fallback = normalizePath(getwd(), winslash = sep))
xdg_data_home(sep = "/", fallback = normalizePath(getwd(), winslash = sep))

Arguments

`sep`	Path separator to be used on Windows
`fallback`	Value to return as fallback (see details)

Value

The following algorithm is used to determine the returned path:

If environment variable (EV) ⁠$XDG_DATA_HOME⁠ exists, return its value
Else, if EV ⁠$HOME⁠ exists, return ⁠$HOME/.local/share⁠
Else, if EV ⁠$USERPROFILE⁠ exists, return ⁠$USERPROFILE/.local/share⁠
Else, return ⁠$fallback⁠

Examples

xdg_data_home()
xdg_data_home()

Package 'toscutil'

Help Index

Get Name of Calling Function

Description

Usage

Arguments

Details

Value

Examples

Capture output from a command

Description

Usage

Arguments

Value

See Also

Examples

Concatenate and Print

Description

Usage

Arguments

Value

Examples

Concatenate and Print

Description

Usage

Arguments

Value

Examples

Concatenate and Print

Description

Usage

Arguments

Value

See Also

Examples

Format and Print

Description

Usage

Arguments

Value

Examples

Format and Print

Description

Usage

Arguments

Value

Examples

Concatenate and Print

Description

Usage

Arguments

Value

Examples

Concatenate and Print

Description

Usage

Arguments

Value

Examples

Concatenate and Print

Description

Usage

Arguments

Value

Examples

Check Documented Functions in a Package

Description

Usage

Arguments

Value

Examples

Get Normalized Configuration Directory Path of a Program

Description

Usage

Arguments

Details

Value

See Also

Examples

Get Normalized Configuration File Path of a Program