Server

First of all we need to have a constantly running server. There are plenty of commercial cloud hosting services, the most ubiquitous being the Amazon Web Services EC2, and it is particularly attractive because of the ‘free tier’ we can use for this project. The caveat is that it’s only free for 12 months. After that you can either spin up another EC2 free tier instance to set up in the same way, or migrate to a Raspberry Pi (at around £30 per slice it’s about the same price as the cheapest EC2 “t2.nano” instance for a year, but you can keep the former as long as you shall live).

For our project we’ll choose AWS, as it allows you to start straight away. Here is a very good tutorial to help you set up your R environment on AWS EC2.

Scheduler

With all Liux systems comes with a utility called cron. It is driven by a crontab (cron table) file, a configuration file that specifies shell commands to run periodically on a given schedule. To edit this file, run:

$ crontab -e

Each line of a crontab file represents a job, and looks like this:

 ┌──────── minute (0 - 59)
 │ ┌──────── hour (0 - 23)
 │ │ ┌──────── day of month (1 - 31)
 │ │ │ ┌──────── month (1 - 12)
 │ │ │ │ ┌──────── day of week (0 - 6) (Sunday to Saturday;
 │ │ │ │ │                                   7 is also Sunday)
 * * * * *  command to execute

The syntax of each line expects a cron expression made of five fields, followed by a shell command to execute.

While normally the job is executed when the time/date specification fields all match the current time and date, there is one exception: if both “day of month” (field 3) and “day of week” (field 5) are restricted (not *), then one or both must match the current day.¹

For example:

# Clears the Apache error log at one minute past midnight (00:01) every day
1 0 * * *  printf > /var/log/apache/error_log

# Runs a shell program called export_dump.sh at 23:45 (11:45 PM) every Saturday
45 23 * * 6 /home/oracle/scripts/export_dump.sh

For our project, we need to run the R code everyday at, say, 9am, so here is the datetime part:

# Run at 9:00 AM on any day of the month, any month and any day of the week
0 9 * * *

Now let’s work out the command to run.

The easest way to run an R script in the command line interface (CLI) is using the command Rscript, e.g.

$ Rscript script.R

Alternatively if the R script is executable then it can be called directly:

$ chmod +x script.R   # make the script executable
$ ./script.R          # the ./ part is necessary

The latter is a more streamline approach, as the command is simply the file name, although the file needs to be referenced by the full directory (e.g. /home/ubuntu/projects/script.R, assumg the script is saved under projects folder, and ubuntu is the default username on the AWS free tier Ubuntu instance). Therefore the crontab should be:

0 9 * * * /home/ubuntu/projects/script.R

The last thing to note is that using the executable script requires specifying the interpreter directive (a.k.a. shebang) at the top of the script #!/usr/bin/env Rscript, this tells the CLI which interpreter to use for the script.²