Beginning R - Files

Everything we’ve done so far has been completely self-contained in the script and every time we run any of them we will get exactly the same output. The power of programming is to be able to take the same piece of code and apply it to different data to get different results. One common way in which this is done is writing a script which can analyse a data file. To do that we need to learn how to open files.

The simplest this we can do with files is read a file in and print it to the screen. Make a new script called file.R and put the following in it:

lines <- readLines(file("file.R"))

for (line in lines){
  print(line)
}

when you run it with Rscript file.R you will see it print out:

[1] ""
[1] "lines <- readLines(file(\"file.R\"))"
[1] ""
[1] "for (line in lines){"
[1] "  print(line)"
[1] "}"

which is (somewhat recursively) the contents of the file file.R

There are a few new things here so let’s go through them in turn. The first thing is to describe the connection to the file. This is specified by file("file.R"), which creates a connection to the file called file.R.

Next, the readLines function is used to open the file and read all of the lines. These are returned as a list, which we assign to a variable called lines, via lines <- readLines(file("file.R")).

If this file does not exist, then readLines will print an error and exit the script, e.g.

lines <- readLines(file("does_not_exist.R"))

Rscript file.R

Error in readLines(file("does_not_exist.R")) : cannot open the connection
In addition: Warning message:
In readLines(file("does_not_exist.R")) :
  cannot open file 'does_not_exist.R': No such file or directory
Execution halted

If the file does exist, then it is opened, all of its lines read into memory, and then closed automatically.

In the next line (for (line in lines)) we are looping over the lines of the file. This loop looks just like those we used when looping over lists a few chapters previously, because lines is just a list containing the lines of the file. We assign the string containing the line from the file to the variable line.

Finally, we print the string line. Note that R will automatically add quotes and backslashes to the lines that are printed. You can remove them by passing quote=FALSE to print, e.g.

lines <- readLines(file("file.R"))

for (line in lines){
  print(line, quote=FALSE)
}

will print

[1] lines <- readLines(file("file.R"))
[1] 
[1] for (line in lines){
[1]   print(line, quote=FALSE)
[1] }

If you want to remove the [1] at the start of each line, then you can print to the screen using cat, specifying that a newline (\n) should be used to separate each line, e.g.

lines <- readLines(file("file.R"))

for (line in lines){
  cat(line, sep="\n")
}

will print the file exactly.

EXERCISE

Printing out R code isn’t the most useful so let’s make a data file to read instead. Make a new file called data.txt and put inside it:

12

54

7

332

54

1

0

(make sure you include a final blank line in the file)

Edit file.R so that it prints out the contents of data.txt instead

Answer

## Data type conversion

Simply reading the data and printing it isn’t very useful. Let’s take a first step towards some data analysis and pretend that the task we’re trying to do is to read in data from the file and add 17 to each value.

lines <- readLines(file("data.txt"))

for (line in lines){
  new_number <- line + 17
  print(new_number)
}

If you edit file.R to contain this code and run it you should see an error:

Error in line + 17 : non-numeric argument to binary operator
Execution halted

This is telling us that there is an error occuring when trying to add 17 to the data read in from the line in the file. The error message says that there is a “non-numeric argument to a binary operator”, which implies that the computer believes that we’re trying to add together something that is not a numeric value. The only two things involved in this operation are line and 17. We know that 17 is an integer, and so is a numeric, so line must be the problematic non-numeric argument.

When reading from a file like this, everything it gives you will always be a string, even if the string only contains digits like “12”. If we know that the file only contains numerics, then we can convert each number to a numeric as it comes in using the as.numeric function:

lines <- readLines(file("data.txt"))

for (line in lines){
  number <- as.numeric(line)
  new_number <- number + 17
  print(new_number)
}

Running this new script will now print out our “processed” data:

[1] 29
[1] 71
[1] 24
[1] 349
[1] 71
[1] 18
[1] 17

EXERCISE

Change file.R to multiply the data by 10 instead of adding 17.

Answer

After looping though the data, print out the sum of all the data values seen.

hint: Make an integer before the loop, initially set to zero and add to it each time around the loop

Answer

Print out the count of the number of data points seen as well.

Answer

Print out the mean average of the data in the file.

Answer

See what happens if you run the script after deleting the contents of data.txt. Add an if statement to fix it.

Answer

Collect the statistics into a summary dictionary with keys sum, count and mean.

Answer

Beginning R - Files

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