Turn a 'cmd_assign' Call Into a Shell Command

Extract a call to cmd_assign() from an R script, and turn it into a shell command.

Usage

extract_shell(path_file, dir_shell = NULL)

Arguments

path_file

Path to the R script containing the call to cmd_assign(). The path starts at dir_shell.

dir_shell

The directory that contains the shell script. The default is the current working directory.

Value

extract_shell() is typically called for its side effect, which is to print a shell command. However, extract_shell() invisibly returns a text string with the command.

The components of a shell command

The shell command produced by extract_shell() normally looks something like this:

Rscript src/model.R \
  data/cleaned.rds \
  out/model.rds \
  --use_log=TRUE

In this command

• Rscript is a call to utils::Rscript();

• \ is a "line continuation character";

• data/cleaned.rds and out/model.rds are unnamed arguments that Rscript passes to src/model.R; and

• --use_log=TRUE is a named argument that Rscript passes to src/model.R

Using extract_shell() to build a data analysis workflow

• Step 1. Write an R script that carries out a step in analysis (eg tidying data, fitting a model, making a graph.) This script will contain a call to cmd_assign(), and will be the first argument passed to Rscript in the shell command. When writing and testing the script, use cmd_assign() interactively.

• Step 2. Once the R script is working correctly, call extract_shell(), and add the command to your shell script.

Location of the shell script

The shell script normally sits at the top level of the project, so that the project folder looks something like this:

workflow.sh
- data/
- src/
- out/
report.qmd

Identifying file arguments

To construct the rule, extract_shell() needs to be able to identify arguments that refer to a file name. To do so, it uses the following heuristic:

• if the call includes arguments whose names start with a dot, then these arguments are assumed to refer to file names;

• otherwise, find arguments whose values actually are file names (as determined by file.exists()) or that look like they could be.

References

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

• Command-Line Programs Introduction to Rscript

• littler Alternative to Rscript

See also

• extract_make() Makefile equivalent of extract_shell()

• shell_script() Create a shell script from calls to cmd_assign()

• cmd_assign() Process command line arguments

• Quick Start Guide How to use cmd_assign()

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

Examples

library(fs)
library(withr)

with_tempdir({

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

  ## add an R script containing a call to 'cmd_assign'
  writeLines(c("cmd_assign(x = 1, .out = 'out/results.rds')",
               "results <- x + 1",
               "saveRDS(results, file = .out)"),
             con = "src/results.R")

  ## call 'extract_shell()'
  extract_shell(path_file = "src/results.R",
                dir_shell = ".")

})
#> Rscript ./src/results.R \
#>   out/results.rds \
#>   --x=1