Wrapper of the Perl module Getopt::Long in R

Description

Wrapper of the Perl module Getopt::Long in R

Usage

GetOptions(..., envir = parent.frame())

Arguments

Details

This function is the same as GetoptLong. It is just to make it consistent as the GetOptions() subroutine in Getopt::Long module in Perl.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
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Wrapper of the Perl module Getopt::Long in R

Description

Wrapper of the Perl module Getopt::Long in R

Usage

GetoptLong(..., help_head = NULL, help_foot = NULL, envir = parent.frame(),
    argv_str = NULL, template_control = list(),
    help_style = GetoptLong.options$help_style)

Arguments

Details

Following shows a simple example. Put following code at the beginning of your script (e.g. foo.R):

    library(GetoptLong)

    cutoff = 0.05
    GetoptLong(
        "number=i", "Number of items.",
        "cutoff=f", "Cutoff for filtering results.",
        "verbose",  "Print message."
    )  

Then you can call the script from command line either by:

    Rscript foo.R --number 4 --cutoff 0.01 --verbose
    Rscript foo.R --number 4 --cutoff=0.01 --verbose
    Rscript foo.R -n 4 -c 0.01 -v
    Rscript foo.R -n 4 --verbose  

In this example, number is a mandatory option and it should only be in integer mode. cutoff is optional and it already has a default value 0.05. verbose is a logical option. If parsing is successful, two variables number and verbose will be imported into the working environment with the specified values. Value for cutoff will be updated if it is specified in command-line.

For advanced use of this function, please go to the vignette.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL

Global options for GetoptLong()

Description

Global options for GetoptLong()

Usage

GetoptLong.options(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

Arguments

Details

Supported global options are following:

config

Configuration of Getopt::Long, check https://perldoc.pl/Getopt::Long#Configuring-Getopt::Long .

template_tag

The tag for identifying specifications in the template. The format should be in left_tag CODE right_tag.

help_style

The style of the help message.

GetoptLong.options(...) should be put before calling GetoptLong function.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL

Directory of current script

Description

Directory of current script

Usage

get_scriptdir()

Value

If the R script is not run from the command-line, it returns NULL.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL

File name of current script

Description

File name of current script

Usage

get_scriptname()

Value

If the R script is not run from the command-line, it returns NULL.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL

Simple variable interpolation in texts

Description

Simple variable interpolation in texts

Usage

qq(..., envir = parent.frame(), code.pattern = NULL, collapse = TRUE, sep = " ")

Arguments

Details

I like variable interpolation in Perl. But in R, if you want to concatenate plain text and variables, you need to use functions such as paste. However, if there are so many variables, quotes, braces in the string you want to construct, it would be painful.

This function allows you to construct strings as in Perl style. Variables are marked in the text with certain rule. qq will look up these variables in user's environment and replace the variable marks with their real values.

For more explaination of this function, please refer to vignette.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

a = 1
b = "text"
qq("a = @{a}, b = '@{b}'")
qq("a = @{a}", "b = '@{b}'", sep = ", ")

a = 1:2
qq("a = @{a}, b = '@{b}'")
qq("a = @{a}, b = '@{b}'", collapse = FALSE)

a = 1
qq("a = `a`, b = '`b`'", code.pattern = "`CODE`")

Global options for qq() related functions

Description

Global options for qq() related functions

Usage

qq.options(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

Arguments

Details

Supported options are following:

cat_prefix

prefix of the string which is printed by qqcat

cat_verbose

whether to print text by qqcat

cat_strwrap

whether call strwrap to wrap the string

code.pattern

code pattern for variable interpolation

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

a = 1
qq.options(cat_prefix = "[INFO] ")
qqcat("a = @{a}\n")
qq.options(cat_verbose = FALSE)
qqcat("a = @{a}\n")
qq.options(RESET = TRUE)
qq.options(code.pattern = "`CODE`")
qqcat("a = `a`\n")
qq.options(RESET = TRUE)

Print a string which has been intepolated with variables

Description

Print a string which has been intepolated with variables

Usage

qqcat(..., envir = parent.frame(), code.pattern = NULL, file = "",
    sep = " ", fill = FALSE, labels = NULL, append = FALSE, cat_prefix = NULL,
    strwrap = qq.options("cat_strwrap"), strwrap_param = list(), sep2 = "")

Arguments

Details

This function is a shortcut of

    cat(qq(text, envir, code.pattern), ...)  

Additionally, you can add global prefix:

    qq.options("cat_prefix" = "[INFO] ")
    qq.options("cat_prefix" = function(x) format(Sys.time(), "[%Y-%m-%d %H:%M:%S] "))
    qq.options("cat_prefix" = NULL)  

You can also add local prefix by specifying cat_prefix in qqcat.

    qqcat(text, cat_prefix = "[INFO] ")  

Please refer to qq to find more details.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

a = 1
b = "text"
qqcat("a = @{a}, b = '@{b}'\n")
qqcat("a = `a`, b = '`b`'\n", code.pattern = "`CODE`")

qq.options("cat_prefix" = function(x) format(Sys.time(), "[%Y-%m-%d %H:%M:%S] "))
qqcat("a = @{a}, b = '@{b}'\n")
Sys.sleep(2)
qqcat("a = @{a}, b = '@{b}'\n")
qq.options(RESET = TRUE)

Source the R script with command-line arguments

Description

Source the R script with command-line arguments

Usage

source_script(file, ..., argv_str = NULL)

Arguments

Examples

# There is no example
NULL