Reproducible Programming in R (2022/23)

Course preparation

There are a few things to do before you can start the course. The details are available in the Guides section of the website under Course preparation. This includes instructions for making sure that R and RStudio are up-to-date and the right packages are installed here, setting yourself up with git and on GitHub here, and installing this (RPiR) package here. We also provide some troubleshooting tips here in case things go a wrong during installation.

Reference materials for the course

These materials are available on moodle, but frankly we don't really like it, so you can find the same (indeed a lot more) information on a reference page here.

Running the course

To start the course, load the RPiR package:

library(RPiR)

You can then see what lectures and practicals are available using:

available_lectures()
available_practicals()

In RStudio, you can also open Preferences..., choose Pane Layout, and tick the box for Tutorial and click OK. Once you have done this, you should find you have a Tutorial pane in RStudio, you can then browse all of the practicals that you have installed there.

Practicals

To run a practical, you can click Start Tutorial from the Tutorial pane in RStudio. You can then run the practical inside that RStudio pane, or click the Show in new window icon in the top left to open it in a larger separate window (you can open multiple practicals simultaneously like this). Alternatively, you can use the run_practical() function in the Console pane. For example, run_practical("practical1-1") will run the first practical of practical series 1.

If you decide to run a practical like this, you will not be able to use the R console until you close it, so we suggest that you open a separate instance of RStudio to run any code, so one RStudio is dedicated to running practicals and lectures.

To reset a practical if you want to start again, click on the Start Over link (look for the tiny grey text below the left menu), which appears if you are not running this inside the Tutorial pane.

To close a practical if you opened it from the Tutorial pane when you have finished it, click on the red STOP button in the Tutorial pane or close the separate window. Clicking instead on the Home icon will return to the practical list, but you can resume the practical from where you left off by restarting it.

To close a practical if you opened it from the Console pane when you have finished it, close the webpage in your web browser, then either hit escape or click on the red STOP button in the RStudio Console to end the process.

If you are having problems with the practicals running correctly, try running RPiR:::clean_cached_exercises() in the Console pane to force the practicals to be rebuilt.

You can also browse the non-interactive practicals on the GitHub website (under Practicals (html)).

Lectures

To view lecture slides, use the run_lecture() function in RStudio. For example, run_lecture("RPiR1-intro") will show the first lecture slides.

You can also see the lectures on the course website using the lecture dropdown menus, either as slides (under Lectures (slides)) or as single continuous documents for later reference (under Lectures (html)).

Course contents

The following core practicals are included in this package:

1. Practical series 1:

   • practical1-1: Exponential growth model; Writing scripts and commenting code
   • practical1-2: Exponential growth model; Writing functions
   • practical1-3: Exponential growth model; Sourcing code
   • practical1-4: Exponential growth model; Generalising and structuring code
   • practical1-5: Births and deaths model; Generalising code
   • practical1-6: Births and deaths model; Writing reports in RStudio

2. Practical series 2:

   • practical2-1: SIS model; Adapting previous code
   • practical2-2: SIS model; Changing the timestep
   • practical2-3: SIS model; Using while() loops
   • practical2-4: SIR model; Adapting previous code

3. Practical series 3:

   • practical3-1: Writing an R package
   • practical3-2: Simple stochastic birth-death model; Using stop()
   • practical3-3: Stochastic birth-death model; Passing functions as arguments
   • practical3-4: Stochastic SIS model
   • practical3-5: Stochastic SIR model
   • practical3-6: Comparing mean stochastic and deterministic SIR models

4. Practical series 4:

   • practical4-1: Creating an R data package
   • practical4-2: Adding some fucntions to a data package
   • practical4-3: Adding a demo

5. Project:

   • project0: Setting up the project repo
   • project1: Creating species richness and Simpson diversity functions
   • project2: Creating a general diversity function
   • project3: Adding in code to cope with Shannon entropy and Berger-Parker
   • project4: Adjusting the diversity function to handle multiple values of q
   • project5: Extending the work to examine properties of subsampled data

As well as the following additional practicals:

• practicalA-1: Introduction to if statements and comparisons
• practicalA-2: Introduction to functions
• practicalA-3: Naming of things
• practicalA-4: Introduction to for and while loops
• practicalA-5: Nested functions