command (version 0.1.3)

shell_script: Create a Shell Script

Description

Create a shell script for a data analysis workflow consisting of commands extracted from existing R files.

Usage

shell_script(
  path_files,
  dir_shell = NULL,
  name_shell = "workflow.sh",
  overwrite = FALSE,
  quiet = FALSE
)

Value

shell_script() is called for its side effect, which is to create a file. However, shell_script() also returns a string with the contents of the shell script.

Arguments

path_files

A path from dir_shell to a directory with R scripts containing calls to cmd_assign().

dir_shell

The directory where shell_script() will create the shell script. If no value is supplied, then shell_script() creates the shell script in the current working directory.

name_shell

The name of the shell script. The default is "workflow.sh".

overwrite

Whether to overwrite an existing shell script. Default is FALSE.

quiet

Whether to suppress progress messages. Default is FALSE.

Details

To create a shell script in the files directory, set files to ".".

To obtain the contents of the shell script without creating a file on disk, creating the file on disk, set name_shell to NULL.

Supplying a value for files is compulsory for shell_script(), but optional for makefile(). The output from shell_script() is generated entirely from files while the output from makefile() also includes some general-purpose Makefile commands.

References

• Episodes 1--3 of The Unix Shell Introduction to the command line

• Command-Line Programs Introduction to Rscript

See Also

• Creating a Shell Script More on shell_script()

• extract_shell() Turn a cmd_assign() call into a shell command

• makefile() Makefile equivalent of shell_script()

• cmd_assign() Process command line arguments

• Modular Workflows for Data Analysis Safe, flexible data analysis workflows

• littler Alternative to Rscript

Examples

library(fs)
library(withr)

with_tempdir({

  ## create 'src'  directory
  dir_create("src")

  ## put R scripts containing calls to
  ## 'cmd_assign' in the 'src' directory
  writeLines(c("cmd_assign(x = 1, .out = 'out/results.rds')",
               "results <- x + 1",
               "saveRDS(results, file = .out)"),
             con = "src/results.R")
  writeLines(c("cmd_assign(x = 1, .out = 'out/more_results.rds')",
               "more_results <- x + 2",
               "saveRDS(more_results, file = .out)"),
             con = "src/more_results.R")

  ## call 'shell_script()'
  shell_script(path_files = "src",
               dir_shell = ".")

  ## shell script has been created
  dir_tree()

  ## print contents of shell script
  cat(readLines("workflow.sh"), sep = "\n")

})