Revisiting cyclones

This is an exercise repository for the Open and Reproducible Science in R module of the MSc in International Health and Tropical Medicine.

In this exercise, we revisit the cyclones dataset and will work on the following tasks.

Task 1: Setup an R project

Although this repository has already been setup for you, unlike other exercises, the structure of the project is yet to be organised.

For this exercise, let’s create appropriate folders/directories based on the workflow we will aim to produce.

1. Create a data directory to store the cyclones dataset into.

2. Create an outputs directory to store the various outputs that we will create in this project.

3. Create a reports directory to store our literate code for reports that we will create in this project.

4. Create an R directory to store all the bespoke functions that we will create for this project.

After completing these steps, git commit and push your changes to your current branch.

Task 2: Download and read the cyclones dataset

The cyclones dataset is not included in this current project unlike before. However the cyclones dataset is available from this URL: https://github.com/OxfordIHTM/teaching_datasets/raw/refs/heads/main/cyclones.xlsx.

Using what you have learned earlier about creating functions, create a function that will download this file into the data folder/directory and will read this dataset into R.

Note that this dataset is in .XLSX format. You will have to use a function that can read an .XLSX file. There is an R package that can be installed that provides a function to read .XLSX files. The name of the package is openxlsx2. Install this package and then use the function called read_xlsx() to read the .XLSX file.

Once you have written the function, use this function in a new R script in the root of the project called cyclones.R.

After completing these steps, git commit and push your changes to your current branch.

Task 3: Perform exploratory data analysis on the cyclones dataset

Now that you have the dataset loaded into R, perform as much exploratory data analysis (EDA) to describe the structure and the variables of the dataset. Some of the explorations you might want to do are:

1. Description of the data such as number of records, any missing values, and description of relevant variables.

2. Summary and distribution of continuous variables.

Write appropriate code in cyclones.R that will provide these summary outputs. Produce appropriate tables and plots.

After completing these steps, git commit and push your changes to your current branch.

Task 4: Write literate code to report your findings

Using Rmarkdown, write literate code to report your EDA findings. Create a file called cyclones.Rmd inside the reports directory that will produce an HTML report/output in the outputs folder.

Once completed, knit your report such that an output HTML is stored in the outputs folder.

After completing these steps, git commit and push your changes to your current branch.