R语言命令行执行代码的3种方式（传递参数和环境变量）

大部分情况在IDE环境中运行R程序，但有时也需要在shell中运行，和其他语言的脚本一样。在shell中如何运行R语言的代码呢？

为了简化使用，把R/Rscript的可执行路径加入path环境变量。（bash，windows cmd）

使用R

首先看看R的help

c:\R> R --arch x64 --help
Usage: Rterm [options] [< infile] [> outfile] [EnvVars]

Start R, a system for statistical computation and graphics, with the
specified options

EnvVars: Environmental variables can be set by NAME=value strings

Options:
  -h, --help            Print usage message and exit
  --version             Print version info and exit
  --encoding=enc        Specify encoding to be used for stdin
  --encoding enc        ditto
  --save                Do save workspace at the end of the session
  --no-save             Don't save it
  --no-environ          Don't read the site and user environment files
  --no-site-file        Don't read the site-wide Rprofile
  --no-init-file        Don't read the .Rprofile or ~/.Rprofile files
  --restore             Do restore previously saved objects at startup
  --no-restore-data     Don't restore previously saved objects
  --no-restore-history  Don't restore the R history file
  --no-restore          Don't restore anything
  --workspace=file      Workspace to be restored
  --vanilla             Combine --no-save, --no-restore, --no-site-file,
                          --no-init-file and --no-environ
  --max-mem-size=N      Set limit for memory to be used by R
  --max-ppsize=N        Set max size of protect stack to N
  -q, --quiet           Don't print startup message
  --silent              Same as --quiet
  --no-echo             Make R run as quietly as possible
  --verbose             Print more information about progress
  --args                Skip the rest of the command line
  --ess                 Don't use getline for command-line editing
                          and assert interactive use
  -f file               Take input from 'file'
  --file=file           ditto
  -e expression         Use 'expression' as input

One or more -e options can be used, but not together with -f or --file

An argument ending in .RData (in any case) is taken as the path
to the workspace to be restored (and implies --restore)

由此可见，R可以接受输入重定向的文件内容，可以通过-f file或--file=file指定文件输入。

有一个选项--args可以提示R跳过之后的参数，其实后面的参数作为传递给R进程。脚本中的
commandArgs()函数可以捕获命令行输入的所有参数。其中，trailingOnly = TRUE只获得–args之后的参数。

命令行还可以定义NAME=value形式的环境变量。环境变量的设置和--agrs无关。

举个栗子： （简单起见，增加--vanilla --no-echo参数）
demo.R内容

cat("\n")
cat("commandArgs(trailingOnly = FALSE)\n")
(args1<-commandArgs(trailingOnly = FALSE))

cat("\n") 
cat("commandArgs(trailingOnly = TRUE)\n")
(args2<-commandArgs(trailingOnly = TRUE))

cat("\n")
cat("get environment variable\n")
Sys.getenv("AAA")
Sys.getenv("BBB")

命令：

R --vanilla --no-echo -f demo.R BBB=hehe  --args AAA=haha

结果：

commandArgs(trailingOnly = FALSE)
[1] "C:\\PROGRA~1\\R\\R-40~1.3/bin/x64/Rterm.exe"
[2] "--vanilla"
[3] "--no-echo"
[4] "-f"
[5] "demo.R"
[6] "BBB=hehe"
[7] "--args"
[8] "AAA=haha"

commandArgs(trailingOnly = TRUE)
[1] "AAA=haha"

get environment variable
[1] "haha"
[1] "hehe"

使用Rscript

先看看Rscript的帮助：

Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args]

--options accepted are
  --help              Print usage and exit
  --version           Print version and exit
  --verbose           Print information on progress
  --default-packages=list
                      Where 'list' is a comma-separated set
                        of package names, or 'NULL'
or options to R, in addition to --no-echo --no-restore, such as
  --save              Do save workspace at the end of the session
  --no-environ        Don't read the site and user environment files
  --no-site-file      Don't read the site-wide Rprofile
  --no-init-file      Don't read the user R profile
  --restore           Do restore previously saved objects at startup
  --vanilla           Combine --no-save, --no-restore, --no-site-file
                        --no-init-file and --no-environ

'file' may contain spaces but not shell metacharacters
Expressions (one or more '-e <expr>') may be used *instead* of 'file'
See also  ?Rscript  from within R

RScript其实R的简化版本，预定义了--no-echo --no-restore -f 和 --args参数。

c:\R>Rscript demo.R BBB=hehe  --args AAA=haha

commandArgs(trailingOnly = FALSE)
[1] "C:\\PROGRA~1\\R\\R-40~1.3\\bin\\x64\\Rterm.exe"
[2] "--no-echo"
[3] "--no-restore"
[4] "--file=demo.R"
[5] "--args"
[6] "BBB=hehe"
[7] "--args"
[8] "AAA=haha"

commandArgs(trailingOnly = TRUE)
[1] "BBB=hehe" "--args"   "AAA=haha"

get environment variable
[1] "haha"
[1] "hehe"

使用R CMD BATCH

c:\R>R CMD BATCH --help
Usage: R CMD BATCH [options] infile [outfile]

Run R non-interactively with input from infile and place output (stdout
and stderr) to another file.  If not given, the name of the output file
is the one of the input file, with a possible '.R' extension stripped,
and '.Rout' appended.

Options:
  -h, --help            print short help message and exit
  -v, --version         print version info and exit
  --no-timing           do not report the timings
  --                    end processing of options

Further arguments starting with a '-' are considered as options as long
as '--' was not encountered, and are passed on to the R process, which
by default is started with '--restore --save'.

Report bugs at <https://bugs.R-project.org>.

R CMD BATCH似乎只能接受输入文件和输出文件，而且默认是--restore --save的参数。

c:\R>R CMD BATCH --no-echo --encoding="UTF-8" demo.R  demo.out --args AAA=haha

没有输出，打开文件demo.out，文件内容是：

commandArgs(trailingOnly = FALSE)
[1] "C:\\PROGRA~1\\R\\R-40~1.3/bin/x64/Rterm.exe"
[2] "-f"                                         
[3] "demo.R"                                     
[4] "--restore"                                  
[5] "--save"                                     
[6] "--no-echo"                                  
[7] "--encoding=UTF-8"                           

commandArgs(trailingOnly = TRUE)
character(0)

get environment variable
[1] ""
[1] ""
> proc.time()
用户 系统 流逝 
0.15 0.04 0.18 

由此可见，R CMD BATCH file不能给file传递参数，也不能传递环境变量。