This template gives you a starting point for structuring a datascience project using R markdown. Clone this repo and knit Main.Rmd to get started.
Having chapters in separate files facilitates collaboration and version control. Also, each chapter imports the same Knitr_setup.Rmd file, so you can knit individual chapters or the main document Main.Rmd with the same settings. Make sure you can knit your chapter independently, because knitting your main document will become slower as your project grows.
In the Data_preparation.Rmd chapter, you may prepare your data an save it e.g. as a .csv file. In your following chapters, you can load the data from the .csv file.
The template renders html files, but it's easy to change it to pdf.