Package 'GetoptLong'

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 <[email protected]>

Examples

# There is no example
NULL

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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 <[email protected]>

Examples

# There is no example
NULL

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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

...	Pass to GetoptLong.
envir	User's enrivonment where GetoptLong looks for default values and exports variables.

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 <[email protected]>

Examples

# There is no example
NULL

---

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

...	Specification of options. The value can be a two-column matrix, a vector with even number of elements or a text template. See the vignette for detailed explanation.
help_head	Head of the help message when invoking Rscript foo.R --help.
help_foot	Foot of the help message when invoking Rscript foo.R --help.
envir	User's enrivonment where GetoptLong looks for default values and exports variables.
argv_str	A string that contains command-line arguments. It is only for testing purpose.
template_control	A list of parameters for controlling when the specification is a template.
help_style	The style of the help messages. Value should be either "one-column" or "two-column".

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 <[email protected]>

Examples

# There is no example
NULL

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Global options for GetoptLong()

Description

Global options for GetoptLong()

Usage

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

Arguments

...	Options, see 'Details' section.
RESET	Whether to reset options to their default values.
READ.ONLY	Whether to only return read-only options.
LOCAL	Whether to switch local mode.
ADD	Whether to add new options.

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 <[email protected]>

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

...	Text string in which variables are marked with certain rules
envir	Environment where to look for variables. By default it is the environment where qq is envoked. It can also be a list in which element names are the variable names to be interpolated.
code.pattern	Pattern of marks for the variables. By default it is @\\{CODE\\} which means you can write your variable as @{variable}. This value can be a vector that all patterns are searched.
collapse	If variables return vector of length larger than one, whether collapse into one string or return a vector
sep	Separator character when there are multiple templates.

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 <[email protected]>

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

...	Options, see 'Details' section.
RESET	Whether to reset options to their default values.
READ.ONLY	Whether to only return read-only options.
LOCAL	Whether to switch local mode.
ADD	Whether to add new options.

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 <[email protected]>

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

...	text string in which variables are marked with certain rules
envir	environment where to look for those variables
code.pattern	pattern of marks for the variables
file	pass to cat
sep	pass to cat
fill	pass to cat
labels	pass to cat
append	pass to cat
cat_prefix	prefix string. It is prior than qq.options(cat_prefix).
strwrap	whether call strwrap to wrap the string
strwrap_param	parameters sent to strwrap, must be a list
sep2	Separation character when there are multiple templates.

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 <[email protected]>

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

file	The R script
...	Pass to source.
argv_str	The command-line arguments.

Examples

# There is no example
NULL

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Setting sub commands

Description

Setting sub commands

Usage

subCommands(..., help_head = NULL, help_foot = NULL, argv_str = NULL)

Arguments

...	Specification of commands. See section Details.
help_head	Head of the help message when invoking Rscript foo.R.
help_foot	Foot of the help message when invoking Rscript foo.R.
argv_str	A string that contains command-line arguments. It is only for testing purpose.

Details

The format of input can be one of the following:

1. A matrix with two columns. Then the first column contains paths of the scripts and the second column contains the description of the subcommand. The basenames of path in the first column by removing the suffix are taken as the sub commands. 2. A matrix with three columns. The the first column contains the sub commands, the second column contains corresponding script paths and the third column contains descriptions of the sub commands. 3. A vector with length as multiples of 2. In this case, every two elements are grouped and concatenated into a matrix by rows. Then it follows the rule 1. 4. A vector with length as multiples of 3. In this case, every three elements are grouped and concatenated into a matrix by rows. Then it follows the rule 2.

Examples

# There is no example
NULL

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