In jr-packages/jrProgBio: Jumping Rivers: Introduction to Programming for Biologists

In this practical we're going to have a go at building a function to automatically create the directory structure we've just talked about in chapter 4.

Question 1

a) We can use the dir.create() function to create a directory in R. Here's a starter function that will create a project directory depending on the users input r create_workflow = function(project_name) { dir.create(project_name) }

b) Now we need to create the directories input, R, graphics and output within the main project directory. To do this we'll need to create the filepath for each. file.path() is a handy function that will help. r file.path("project", "directory") r create_workflow = function(project_name) { dir.create(project_name) for (directory in c("input", "R", "graphics", "output")) { dir.create(path = file.path(project_name, directory)) } }

c) Now we need to create the R scripts load.R, clean.R, func.R, do.R and graphics.R within the R directory. The file.create() function can create files of any extension. So to create an R file we could do r file.create("load.R") and this will create an empty R script called load.R. Hint: You can do this with a for loop. Remember your file paths! r create_workflow = function(project_name) { dir.create(path = project_name) for (directory in c("input", "R", "graphics", "output")) { dir.create(path = file.path(project_name, directory)) } for (rfile in c("load", "clean", "func", "do", "graphics")) { fname = paste0(rfile, ".R") fpath = file.path(project_name, "R", fname) file.create(fpath) } }

Question 2 - Harder

This question is much harder than the first, you have been warned! It would be ideal if we could insert the source commands into the R scripts as well. You can append lines of text to a file using the writeLines(), file() and close() functions. For instance,

file.create("clean.R")
file_conn = file("clean.R")
writeLines("source('load.R')", file_conn)
close(file_conn)

\noindent The contents of each file should look like so:

• load.R - empty
• clean.R - One line of code: source("project_name/R/load.R")
• func.R - One line of code: source("project_name/R/clean.R")
• do.R - One line of code: source("project_name/R/func.R")
• graphics.R - One line of code: source("project_name/R/do.R")

The idea being that when you call source("do.R") in graphics.R, it will run all four previous files.

create_workflow = function(project_name) {
  dir.create(path = project_name)
  for (directory in c("input", "R", "graphics", "output")) {
    dir.create(path = file.path(project_name, directory))
  }
  for (rfile in c("load", "clean", "func", "do", "graphics")) {
    fname = paste0(rfile, ".R")
    fpath = file.path(project_name, "R", fname)
    file.create(fpath)
    if (exists("code")) {
      print(exists("code"))
      file_conn = file(fpath)
      writeLines(code, file_conn)
      close(file_conn)
    }
    code = paste0('source("', fpath, '")')
  }
}

Solutions

Solutions are contained within this package:

vignette("solutions4", package = "jrProgramming")

jr-packages/jrProgBio documentation built on Jan. 18, 2020, 1:32 a.m.