rscripting: rscritping: convenience tools for Rscript and more

In BigelowLab/rscripting: Simple tools for scripting with Rscript

rscritping: convenience tools for Rscript and more

Description

The rscritping package provides a numbr of conveneince tools to help the developer manage scripting, argument parsing, timing, file archiving and the like.

Argument parsing

Convenience handling of Rscript arguments modeled after Python's argparse module. Provides CommandArgsRefClass and ArgumentsRefClass for managing arguments. A simple example is provided below. See argparse for inspiration... http://docs.python.org/dev/library/argparse.html

Logging

A simple logger to allow info/warn/error messaging. Logged messages are possibly sent to a regular file, but the user can opt to echo the messages to the console. Also included is a simple StopwatchRefClass class for multi-part timing as well as a TimekeeperRefClass which will manage one or more stopwatches. Here is a rough outline of the 'is-as' 'has-a' relationships among these classes

• A LoggerRefClass object contains a TimekeeperRefClass object.

• A TimekeeperRefClass object contains a list of one or more StopwatchRefClass objects referred to by name or index position

• A StopwatchRefClass contains one or more intervals referred to by 'interval' name or index position

Configurations

A small set of tools for managing configuration files, formatted like INI files in Windows. See http://effbot.org/librarybook/configparser.htm and http://docs.python.org/release/2.6.8/library/configparser.html for inspiration.

Examples

## Not run:    
###
#  Using CommandArgs
###

   # define a vector of arguments, usually the value of commandArgs(trailingOnly = FALSE) 
   # but in this example we have contrived a variety of space-delimited arguments
   
   args <- c("/Library/Frameworks/R.framework/Resources/bin/exec/R", "--slave", 
      "--no-restore", "--vanilla", 
      "--file /Users/Shared/code/R/test-scripts/commandArgs.Rscript", 
      "--args", "-bob", "-no-bob" , "zip=", "itty", "doodah")
   
   # define a function called when the value of an argument is retrieved, you'll 
   # see this when we define the 'dog' argument below. Note that the first argument 
   # is the ArgumentRefClass object and the the value is the first element of the 
   # \code{value} field which may more than one element.
   squareDog <- function(x, ...){
      x$value[[1]]^2
   }
   
   # create CommandArgs instance using our dummy arguments
   X <- CommandArgs(args)
   
   # define 4 different arguments, two logicals, one with an 'action' 
   #  and one with multiple elements 
   X$add_argument("bob", type = "set_true", default = FALSE)
   X$add_argument("nobob", flag = "--no-bob", type = "set_false", default = TRUE)
   X$add_argument("dog", type = "numeric", default = 3, 
      required = FALSE, action = 'squareDog')
   X$add_argument("zip", type = "character", narg = 2, 
      choices = c("itty", "bitty", "doodah", "boom"), default = "boom")
   
   #run the parser
   X$parse_arguments()
   
   # print the whole shebang
   X$show()
   
   #  get the values of the arguments
   X$get("dog")
   X$get("bob")
   X$get("zip")

###
#  Using Configurator
###

   Here's an example from SCGC's setup tool, 'install-packages.Rscript'
   whcih expects a '~/.Rinstallrc' configuration file like the following

   [lib_path]
   user=/Users/ben/Library/R/3.0/library
   system=/Library/Frameworks/R.framework/Versions/3.0/Resources/library
   [download_uri]
   ben_dropbox=https://dl.dropboxusercontent.com/u/8433654/packages
   [packages]
   commandArguments=commandArguments_0.1.tar.gz
   configurator=configurator_0.1.tar.gz
   ...

   X <- Configurator('~/.Rinstallrc')
   X$get('download_uri', 'ben_dropbox')
   X$set('download_uri', 'bbc', 'http://www.bbc.com/')


###
#  Using Logger
###
   X <- Logger(name = 'logger-example', file = 'test.log', start_watch = TRUE)
   X$warn( "You gotta big problem here!", do_sprintf = FALSE)
   X$info("I like %s", "sailing", do_timestamp = FALSE)
   X$error("I ate all the %0.2f", pi, do_echo = FALSE)
   X$elapsed() 

###
#  Using Stopwatch
###   
   # An example with Stopwatch
   SW <- Stopwatch(name = 'timex', start = FALSE)
   #start it
   SW$start()
   SW$elapsed()
   SW
   Sys.sleep(2)
   # When stopping you can name the interval for later retreival
   SW$stop(interval = 'first')
   SW
   SW$elapsed(interval = "first")
   SW$start()
   Sys.sleep(2)
   SW$stop(interval = "second")
   Sys.sleep(1)
   SW$elapsed(interval = 'second')
   SW$elapsed(interval = 'first')
   # now accumulate the elapsed times
   SW$elapsed(accumulate = TRUE)

###
#  Using Stopwatch
###      
   # An example with 
   # create a container class, starting a stopwatch right away
   timer <- Timekeeper(start_watch = TRUE, name = 'master')
   Sys.sleep(3)
   # add another stopwatch
   timer$start("two")
   timer
   timer$stop("two", interval = "another")
   timer$elapsed("master")

## End(Not run)

BigelowLab/rscripting documentation built on Oct. 24, 2022, 5:31 p.m.