Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Compound assignment pipe operator

Description

See magrittr::%<>% for details.

Usage

lhs %<>% rhs

Bullets

Description

Bullets

Usage

.bullets()

Value

A list of various coloured bullets

Creates a title bar

Description

Creates a title bar

Usage

.get_title_bar(left = NULL)

Arguments

Value

A string vector of a title bar of 80 characters.

Find duplicated packages names

Description

Find duplicated packages names

Usage

.pkg_duplicated(pkgs)

Arguments

Value

A named list of duplicated names and number of occurrences

Extracts the matches from stringr::str_match[_all]

Description

Extracts the matches from stringr::str_match[_all]

Usage

.regexl(result)

Arguments

Value

a list of matches

Add badges to the README file for use on Github

Description

Add badges to the README file for use on Github

Usage

add_badges(
  github_pkg,
  states = c("active", "abandoned", "concept", "inactive", "moved", "suspended",
    "unsupported", "wip"),
  readme_file = "README.md",
  show_repo_status = TRUE,
  show_cran_version = TRUE,
  show_package_version = TRUE,
  show_min_r = TRUE,
  show_last_update = TRUE,
  show_travis = TRUE,
  show_code_coverage = TRUE
)

Arguments

Examples

## Not run: 
add_badges("hvdboorn/hgutils")

## End(Not run)

Analyze package imports

Description

Analyzes the package imports via library() and load_packages() in a list of filenames.

Usage

analyze_package_imports(
  files = list.files(pattern = "\\.[rR]$", recursive = TRUE)
)

Arguments

Value

a named list of results (invisibly). This list contains all import statements, a list of duplicated imports, a list of redundant imports, all function calls in the files with the corresponding imports and a list of packages with the number of function calls.

Examples

## Not run: 
analyze_package_imports(list.files(pattern="\\.[rR]$", recursive=TRUE))

## End(Not run)

Text representation of patient inclusion flowchart

Description

Text representation of patient inclusion flowchart

Usage

## S3 method for class 'patient_flowchart'
as.character(x, length = 7, ...)

Arguments

Assign variables in a list

Description

Assign variables in a list

Usage

assign_list(x, envir = .GlobalEnv)

Arguments

Examples

assign_list(list(a=1, b=2))

Table one

Description

Table one

Usage

create_table_one(df, numbers_as_categories = TRUE, deaths = NULL)

create_contigency_table(df, x, max_size = 8, numbers_as_categories = TRUE, ...)

percentage_table(x, n_digits = 2)

Arguments

Value

A dataframe containing the contingency tables for each of the variables in df.

A matrix with distinct (factor) labels and corresponding counts and percentages.

Creates a text table

Description

Creates a text table

Usage

create_text_table(string, table_width = 80, compact = TRUE)

Arguments

Value

A vector of strings per row, forming together a table.

See Also

get_square_grid.

Examples

cat(create_text_table(LETTERS),sep = "\n")

Set imports for DESCRIPTION file

Description

Update the DESCRIPTION file with all imported packages stated in the source code.

Usage

crossref_description(
  skip_prompt = FALSE,
  update = TRUE,
  use_version_numbers = TRUE,
  rversion = "DEPENDENCIES_VERSION"
)

Arguments

Value

Invisibly returns a list with the current R version, the R version obtained from dependencies and packages names (including version numbers).

See Also

numeric_version

Other developer functions: generic_implementations(), load_packages(), update_settings(), valid_pkgname()

Examples

## Not run: crossref_description(skip_prompt=TRUE)

Default value

Description

Returns a default value for a scalar, to be used when the input is NA, NULL or has a length of 0.

Usage

default(x, default_value)

Arguments

Value

The value of x when x is not NA, NULL or has a length of 0, and default_value otherwise.

Examples

default(NA, 0)

Description functions

Description

Read, write and update the DESCRIPTION file. read.description reads the DESCRIPTION file in the current project directory and returns a named list. write.description writes the named list back to disk, overwriting the current DESCRIPTION file. Finally, update_description combines both functions by reading the DESCRIPTION file, updating or creating a field and writing the result back to disk.

Usage

read.description()

write.description(description)

update_description(fieldname, value, after = NULL)

Arguments

Details

The 'Depends', 'Imports' and 'Suggests' fields are sorted before writing the DESCRIPTION file.

Examples

## Not run: 
description = read.description()
write.description(read.description())

#update date in description file
update_description("Date", format(Sys.Date(), "%Y%-%m-%d"))

## End(Not run)

Discretize continuous numbers

Description

Discretize continuous numbers

Usage

discretize_numbers(x, min_size = 1, ...)

Arguments

Details

The function get_breaks is called to create the boundaries between groups. It is called on default with limits = range(x) and with include_bounds = FALSE. This behaviour may be overridden with the ... argument, although it is advised not to do so to avoid empty groups.

NA values are preserved in the result.

Value

A factor with the same length as x, with labels indicating bins.

Examples

ages = round(rnorm(1000,50,10)); ages[1] = NA
discretize_numbers(ages)

Format time duration

Description

Format time duration

Usage

format_duration(start, end = Sys.time())

Arguments

Value

A string representation of the duration.

Format variable value

Description

Creates a nice string representation of a variable value.

Usage

frmt(x, show_class = FALSE, use_quotes = TRUE)

Arguments

Value

A character vector with the string representation of x.

Examples

frmt(c(1,2,3))

Retrieve generic function implementations

Description

Obtains a list of classes for which the supplied generic function has an implementation.

Usage

generic_implementations(generic, remove_default = TRUE)

Arguments

Value

A vector with class names for which argument 'generic' has an implementation.

Note

Removes the default generic implementation

See Also

Other developer functions: crossref_description(), load_packages(), update_settings(), valid_pkgname()

Examples

#get a list of classes which have an implementation for graphics::plot
impls = generic_implementations('plot')

Create nice axis breaks for plots

Description

Set the breaks for a graph in nice positions.

Usage

get_breaks(
  limits,
  N = 10,
  max_breaks = 10,
  int_only = TRUE,
  multiples_only = FALSE,
  include_bounds = TRUE
)

Arguments

Details

get_breaks is the base function and creates a vector of breaks ggplot_breaks is a wrapper and makes usage easier in ggplot2. The limits of the axis may not be known beforehand, but ggplot_breaks receives it from ggplot and then creates nice breaks.

Value

A sorted numerical vector with breaks of length |max_breaks|+2 when include_bounds is TRUE and of size |max_breaks| otherwise.

Examples

get_breaks(24, N=12, max_breaks=15)

## Not run: 
ggplot() + scale_x_continuous(breaks = ggplot_breaks(N=12, max_breaks=15))
## End(Not run)

Specifies a square grid which fits N objects.

Description

The resulting grid will be of size a*a or a*(a+1) where a is an integer. It will therefore always be a square or or have one row/column more than columns/rows.

Usage

get_square_grid(N, moreRows = TRUE)

Arguments

Value

A named list with elements rows and columns specifying the size of the optimal grid.

Examples

get_square_grid(5)

Patient flowchart

Description

Creates a patient flowchart which visualizes exclusions and updates the dataset.

Usage

inclusion_flowchart(
  dataset,
  node_text = "%s eligable patients",
  stratum = NULL
)

exclude_patients(
  flowchart,
  dataset,
  exclusion_criterium,
  reason = deparse(substitute(exclusion_criterium)),
  node_text = "%s eligable patients",
  excluded_text = "%s excluded"
)

Arguments

Value

A flowchart (when creating the flowchart), or updated dataset (when excluding patients).

Note

When excluding patients, the flowchart is updated 'behind the scenes' and is not returned.

Examples

## Not run: 
dataset = survival::lung; dataset$sex = factor(dataset$sex,labels=c("male","female"))
flowchart = inclusion_flowchart(dataset)
dataset = exclude_patients(flowchart, dataset, status==1) #exclude all patients who did not die
dataset = exclude_patients(flowchart, dataset, time<100) #exclude patients with a short follow-up
flowchart #print diagram

## End(Not run)

List package collections

Description

List package collections

Usage

load_package_collection(
  collection_name = names(list_package_collections()),
  ...
)

list_package_collections()

list_common_packages()

load_common_packages(...)

Arguments

Load and install packages

Description

Utility function to load and optionally install packages if they are missing. When the function terminates, packages are installed (if necessary) and loaded. Upgradeable packages are shown.

Usage

load_packages(
  ...,
  install_packages = TRUE,
  force_install = FALSE,
  show_outdated_packages = FALSE,
  default_loading_method = FALSE,
  return_library_statements = FALSE
)

Arguments

Details

load_packages optionally installs, upgrades and attaches packages to the work space for a list of specified packages.

Value

Returns invisibly a list with additional package information and results of installing/upgrading and loading.

See Also

install.packages for installation of new packages, update.packages for updating outdated packages, library for load and attaching packages.

Other developer functions: crossref_description(), generic_implementations(), update_settings(), valid_pkgname()

Examples

## Not run: 
# Package names given one-by-one or in a vector
load_packages(c('magrittr', 'dplyr'))
load_packages('magrittr', 'dplyr')

# Package names may be unquoted
load_packages(magrittr, dplyr)
load_packages('magrittr','dplyr', install_packages=FALSE)

## End(Not run)

Standardized message colours

Description

Standardized message colours

Usage

.cinfo(...)

.cinfo_bg(...)

.cwarn(...)

.cwarn_bg(...)

.chint(...)

.chint_bg(...)

.csucc(...)

.csucc_bg(...)

.cfail(...)

.cfail_bg(...)

.cnumb(...)

.cnumb_bg(...)

Arguments

Value

A function to colour text

Display coloured messages

Description

Display coloured messages

Usage

mess_info(header, message, pre = "")

mess_succ(header, message, pre = "")

mess_fail(header, message, pre = "")

mess_warn(header, message, pre = "")

mess_numb(header, message, pre = "")

mess_hint(message, header = "", pre = "")

Arguments

Value

A coloured message.

Print the patient inclusion flowchart

Description

Print the patient inclusion flowchart

Usage

## S3 method for class 'patient_flowchart'
print(x, length = 7, ...)

Arguments

Print a formatted percentage table

Description

Print a formatted percentage table

Usage

## S3 method for class 'percentage_table'
print(x, ...)

Arguments

Examples

print(percentage_table(iris$Species))

Creates an animated progress bar

Description

Creates an animated progress bar

Usage

progressbar(
  format = "[[|][|/-\\][ ]]",
  width = 20,
  refresh = 200,
  n_iterations = NULL
)

render(object, ...)

## S3 method for class 'fraction_progressbar'
render(object, progress, show_progress = c("nothing", "percentage"), ...)

## S3 method for class 'iteration_progressbar'
render(
  object,
  progress,
  show_progress = c("nothing", "percentage", "iteration"),
  ...
)

## S3 method for class 'progressbar'
render(object, show_progress = c("nothing", "percentage", "iteration"), ...)

Arguments

Details

The format of the progress bar is given by a character vector. It consists of 5 parts:

1. the left border of the progress bar consisting of 0 or more characters.

2. a pair of square brackets containing a single character which represents the loaded area.

3. a pair of square brackets containing 0 or more characters. These are animated on the border between the loaded and unloaded area.

4. a pair of square brackets containing a single character which represents the unloaded area.

5. the right border of the progress bar consisting of 0 or more characters.

The format follows the following regular expression: ^.*?[.?][.*?][.?].*$

Examples

## Not run: 
# simple progressbar
bar = progressbar(format = "[[|][|/-\\][ ]]")
# fancy progressbar using UTF-8 codes
n_operations = 1000
bar2 = progressbar(format="\u25ba[\u2589][\u2580\u2584][\u3000]\u25c4", n_iterations=n_operations)

for(i in 1:n_operations) {
  cat("\r", render(bar),sep="")
  Sys.sleep(0.01)
}
## End(Not run)

Creates a progression calculator which can display a loading bar and expected time to completion

Description

Creates a progression calculator which can display a loading bar and expected time to completion

Usage

progression_calculator(task_description, N)

## S3 method for class 'progression_calculator'
render(object, i, interval = 10, ...)

Arguments

Examples

## Not run: 
#create progression calculator with 10 iterations
progress = progression_calculator("Example", N=10)
for(i in 1:10) {
  render(progress, i, interval=1) #render the calculator
  Sys.sleep(0.2)
}

## End(Not run)

Find redundant packages

Description

Find redundant packages

Usage

redundant_packages(packages)

Arguments

Details

Certain packages have a direct dependency on other packages. In that case it is unnecessary to attach the latter packages. This function finds those packages and returns them in a named list. For each named item, the name is imported by the value in the list.

Value

A named list of packages names, where each value is a vector of packages already loading the corresponding package.

Examples

## Not run: 
#grid does not have be loaded since gridGraphics already does so.
redundant_packages(c("gridGraphics","grid"))

## End(Not run)

Remove empty rows

Description

Remove empty rows

Usage

rm_empty_rows(dataframe)

Arguments

Value

A data.frame with rows removed that only contain NA.

See Also

Other NA functions: rm_na()

Examples

data <- rbind(c(1,2,3), c(1, NA, 4), c(4,6,7), c(NA, NA, NA), c(4, 8, NA))
rm_empty_rows(data)

Remove NA

Description

Remove NA

Usage

rm_na(x)

Arguments

Value

Vector without NA

See Also

Other NA functions: rm_empty_rows()

Examples

rm_na(c(1,2,NA,54))

Round number

Description

Rounds a number to a specified amount of digits and returns the string value.

Usage

rnd_dbl(dbl, digits = 3)

Arguments

Value

A string value of the number rounded to the specified amount of digits.

Examples

rnd_dbl(1.26564,digits = 2)

Adds comma's to separate thousands in numbers

Description

Adds comma's to separate thousands in numbers

Usage

sep_thousands(n)

Arguments

Value

A string with the number and thousands separated by comma's.

Examples

sep_thousands(13243.33) #13,243.33

Creates an animated spinner

Description

Creates an animated spinner

Usage

spinner(format = "|/-\\", refresh = 200)

## S3 method for class 'spinner'
render(object, ...)

Arguments

Details

The format of the spinner simply consists of the characters in order which the spinner cycles through.

Examples

## Not run: 
sp = spinner("|/-\\")
n_operations = 100

for(i in 1:n_operations) {
  cat("\r", render(sp),sep="")
  Sys.sleep(0.01)
}
## End(Not run)

Cleans R for use

Description

Clears workspace, deletes all objects from global environment, clears graphics and (optionally) sets working directory.

Usage

startup(
  removeObjects = TRUE,
  runGarbageCollection = TRUE,
  clearGraphics = TRUE,
  folder = NULL,
  verbose = TRUE,
  seed = 37
)

Arguments

Examples

## Not run: startup()

S.T.F.U.: Stop Text From turning Up

Description

S.T.F.U.: Stop Text From turning Up

Usage

stfu(expr)

Arguments

Value

Returns invisibly the result of expr.

Warning

Make sure to call this function always directly on the expression and never indirectly e.g. via pipes. Example: stfu(expr) is correct, but expr %>% stfu will not hide the output. However, the expr argument itself may contain pipes.

Examples

stfu(print("hi"))

Translate item

Description

Translate item

Usage

translate_items(vector, dict)

Arguments

Value

A vector with new values

Examples

v = c("A","B","C")
dict = c("A"="1")

translate_items(v, dict)

Update default function settings

Description

Uses ellipsis parameter to update a list of default settings.

Usage

update_settings(default, ...)

Arguments

Value

The updated list of settings with updated values.

See Also

Other developer functions: crossref_description(), generic_implementations(), load_packages(), valid_pkgname()

Examples

foo = function(...) {
  default = list(a=1)
  settings = update_settings(default, ...)
}

## Not run: foo(a=2, b=3)

Validate package and function names

Description

Naming rule obtained from 'Writing R Extensions' manual. The corresponding regular expression used for verifying the package name is "[[:alpha:]][[:alnum:]\.]*[[:alnum:]]". For function names this is "((?:[[:alpha:]]|\.(?![0-9]))[[:alnum:]_\.]*)"

Usage

valid_pkgname(pkg)

valid_funcname(func)

Arguments

Value

A named logical indicating whether the package name is valid.

References

make.names, 'Writing R Extensions' manual.

See Also

Other developer functions: crossref_description(), generic_implementations(), load_packages(), update_settings()

Examples

valid_pkgname("hgutils") # valid
valid_pkgname("ggplot2") # valid
valid_pkgname("pkg2.-1") # invalid

valid_funcname(".hgutils") # valid
valid_funcname("ggplot2") # valid
valid_funcname(".2pkg") # invalid

Wrap string table

Description

Wrap string table

Usage

wrap_text_table(string, exdent, min_size = 9, table_width = 80 - exdent)

Arguments

Value

A character vector of a wrapped table where rows are separated by the newline character.

See Also

str_wrap, get_square_grid.

Examples

cat(wrap_text_table(LETTERS, exdent=0))