Overview

This repository reflects the materials and methods used in the exercise assigned for Module 8 (Fitting Basic Statistical Models) in MADA 2021.

Pre-requisites

This repository is created from a template for a data analysis project using R, Rmarkdown (and variants, e.g. bookdown), Github and a reference manager that can handle bibtex. It is also assumed that you have a word processor installed (e.g. MS Word or LibreOffice). You need that software stack to make use of this repository.

Repository structure

• All data are in the subfolders inside the data folder.
• All code is in the code folder or subfolders.
• All results (figures, tables, computed values) are in results folder or subfolders.
• See the various readme.md files in those folders for some more information.

Repository content

• The original data is in the raw_data folder.
• The processing_code folder contains an R script which load the raw data, perform a bit of cleaning, and save the result in the processed_data folder.
• The analysis_code folder contains three different codes to analyze the data. See the readme.md in the folder for more information.

Repository navigation and replication

• Start with the processing_code folder in the code folder to import and clean/wrangle the raw data.
• Follow the readme.md file in the code folder to follow analysis coding order.
• The scripts and markdown files will save the results of the analysis in the results folder.

Data information

• The raw data for this exercise comes from the following citation: McKay, Brian et al. (2020), Virulence-mediated infectiousness and activity trade-offs and their impact on transmission potential of patients infected with influenza, Dryad, Dataset, https://doi.org/10.5061/dryad.51c59zw4v.
• The data dictionary is included in this repository as well.
• This analysis focuses on two outcomes: body temperature (continuous) and nausea (categorical).