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R 设置外部变量参数,打包小脚本

R 设置外部变量参数,打包小脚本

作者: Peter_iris | 来源:发表于2021-05-24 18:25 被阅读0次

    不管是使用shell,python,R 我们都希望写的小脚本能够多次使用,不是说每次使用都要从头写起,这个时候,就需要考虑怎么把外部的数据如何传到脚本中,类似命令行程序。shell 进行传参是利用$1,$2,$3等传入的,可读写性太差,处理一些小问题还可以,但是长时间做的可能自己就看不懂自己里面写了什么东西。而python开发了argparse 包,可以用于外部变量的传入,R则也参照Python的路子利用optparse 包实现了小脚本的外部传参。那么,这个传参的函数应该如何写呢?


    R 设置传参格式

    To install the last version released on CRAN use the following command:

    install.packages("optparse")
    

    To install the development version use the following command:

    install.packages("remotes")
    remotes::install_github("trevorld/r-optparse")
    

    Dependencies

    The package dependents on the R package: getopt

    An example

    library("optparse")
    option_list <- list( 
        make_option(c("-v", "--verbose"), action="store_true", default=TRUE,
                      help="Print extra output [default]"),
        make_option(c("-q", "--quietly"), action="store_false", dest="verbose", 
                      help="Print little output"),
        make_option(c("-c", "--count"), type="integer", default=5,
                     help="Number of random normals to generate [default %default]",
                    metavar="number"))
    
    args<-parse_args(OptionParser(option_list=option_list), args = c("--verbose", "--count=11"))
    

    optparse automatically creates a help option:

    Rscript  mhap.R  -h
    
    Usage: %prog [options]
    
    Options:
        -h, --help
            Show this help message and exit
    
        -v, --verbose
            Print extra output [default]
    
        -q, --quietly
            Print little output
    
        -c NUMBER, --count=NUMBER
            Number of random normals to generate [default 5]
    

    options 变量类型的设置

    在参数变量的设置中,有如下几个参数可供设置:
    常规主要设置参数:long_flag, action, type, default, help


    short_flag
    String of the desired short flag comprised of the“-” followed by a letter.

    long_flag
    String of the desired long flag comprised of “--”followed by a letter and then a sequence of alphanumeric characters.

    action
    A character string that describes the action optparse should take when it encounters an option, either“store”, “store_true”, or “store_false”. The default is “store”which signifies that optparse should store the specified following value if the option is found on the command string. “store_true” stores TRUE if the option is found and “store_false” stores FALSE if the option is found.

    type
    A character string that describes specifies which data type should be stored, either “logical”, “integer”, “double”, “complex”, or “character”. Default is “logical” if action %in% c("store_true", "store_false"), typeof(default) if action == "store"and default is not NULL and “character” if action == "store" and default is NULL. “numeric” will be converted to “double”.

    dest
    A character string that specifies what field in the list returned by parse_args should optparse store option values. Default is derived from the long flag in opt_str.

    default
    The default value optparse should use if it does not find the option on the command line.

    help
    A character string describing the option to be used by print_help in generating a usage message. %default will be substituted by the value of default.

    metavar
    A character string that stands in for the option argument when printing help text. Default is the value of dest.

    callback
    A function that executes after the each option value is fully parsed

    callback_args
    Additional arguments that pass to the callback function.


    上面例举了optparse R包中用来构建外部传参函数的参数,这些参数共同组成一个外部变量参数的list,以供后续调用。对于这个list的构建,可添加add_option,可新建make_option.

    add_option adds a option to a prexisting OptionParser instance, whereas make_option is used to create a list of OptionParserOption instances that will be used in the option_list argument of the OptionParser function to create a new OptionParser instance.

    Both make_option and add_option return instances of class OptionParserOption.

    Usage:

    make_option( opt_str,   action = NULL,  type = NULL,   dest = NULL, default = NULL,   help = "",
                metavar = NULL,  callback = NULL,  callback_args = NULL
                )
    add_option( object,  opt_str,  action = NULL,  type = NULL,  dest = NULL,  default = NULL,
                help = "",  metavar = NULL,  callback = NULL,  callback_args = NULL
                )
    

    Examples

    library("optparse")
    parser <- OptionParser()
    
    ### case one
    parser <- add_option(parser, c("-v", "--verbose"), action="store_true", 
                    default=TRUE, help="Print extra output [default]")
    parser <- add_option(parser, c("-q", "--quietly"), action="store_false", 
                        dest="verbose", help="Print little output")
    parser <- add_option(parser, c("-c", "--count"), type="integer", default=5, 
                    help="Number of random normals to generate [default %default]",
                    metavar="number")
    parse_args(parser, args = c("--quietly", "--count=15"))
    
    ###case two
    # NOT RUN {
       make_option("--longflag")
       make_option(c("-l", "--longflag"))
       make_option("--integer", type = "integer", default = 5)
       make_option("--integer", default = as.integer(5))  # same as previous
    
       # examples from package vignette
       make_option(c("-v", "--verbose"), action = "store_true", default = TRUE,
           help = "Print extra output [default]")
       make_option(c("-q", "--quietly"), action = "store_false",
         dest = "verbose", help = "Print little output")
       make_option(c("-c", "--count"), type = "integer", default = 5,
           help = "Number of random normals to generate [default %default]",
           metavar = "number")
       make_option("--generator", default = "rnorm",
           help = "Function to generate random deviates [default \"%default\"]")
       make_option("--mean", default = 0,
           help = "Mean if generator == \"rnorm\" [default %default]")
       make_option("--sd", default = 1, metavar = "standard deviation",
           help = "Standard deviation if generator == \"rnorm\" [default %default]")
    # }
    

    Reference:

    https://www.rdocumentation.org/packages/optparse/versions/1.6.6
    https://docs.python.org/3/library/optparse.html

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