R 设置外部变量参数，打包小脚本

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？

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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