Project Management with RStudio

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Edward Johnson
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1 Project Management with RStudio Tzu L. Phang

2 Project Management with RStudio: Overview Goto Class link to follow along Questions How can I manage my projects in R? Objectives To be able to create self-contained projects in RStudio To be able to use git from within RStudio

3 Why Project Management? There are many reasons why we should ALWAYS avoid this: It is really hard to tell which version of your data is the original and which is the modified; It gets really messy because it mixes files with various extensions together; It probably takes you a lot of time to actually find things, and relate the correct figures to the exact code that has been used to generate it; A good project layout will ultimately make your life easier: It will help ensure the integrity of your data; It makes it simpler to share your code with someone else (a lab-mate, collaborator, or supervisor); It allows you to easily upload your code with your manuscript submission; It makes it easier to pick the project back up after a break.

4 RStudio Solution We re going to create a new project in RStudio: Click the File menu button, then New Project. Click New Directory. Click Empty Project. Type in the name of the directory to store your project, e.g. my_project. Make sure that the checkbox for Create a git repository is selected. Click the Create Project button. Now when we start R in this project directory, or open this project with RStudio, all of our work on this project will be entirely self-contained in this directory

5 Best Practices for Project Organization Treat data as read only Data is typically time consuming and/or expensive to collect Working with them interactively (e.g., in Excel) where they can be modified means you are never sure of where the data came from, or how it has been modified since collection It is therefore a good idea to treat your data as read-only. Data Cleaning Raw data are dirty ; need to clean to a format R can use (data munging) Useful to store cleaning script in separate folder, and create a 2nd read-only data folder to hold the cleaned data sets Treat generated output as disposible Anything generated by your scripts should be treated as disposable: it should all be able to be regenerated from your scripts.

6 Good Enough Practices for Scientific Computing Good Enough Practices for Scientific Computing gives the following recommendations for project organization: Put each project in its own directory, which is named after the project. Put text documents associated with the project in the doc directory. Put raw data and metadata in the data directory, and files generated during cleanup and analysis in a results directory. Put source for the project s scripts and programs in the src directory, and programs brought in from elsewhere or compiled locally in the bin directory. Name all files to reflect their content or function.

7 ProjectTemplate - a possible solution A third-party package: ProjectTemplate: to set up an ideal directory structure for project management. Enable analysis pipeline/workflow organized and structured Enable tracking and sharing of project (with git) To use ProjectTemplate Install ProjectTemplate. install.packages( ProjectTemplate ) Load the library library(projecttemplate) Initialise the project create.project(../my_project, merge.strategy = allow.non.conflict )

8 Challenges Goto class material by clicking here Do Challenge 1 and Challenge 2

9 Version Control We also set up our project to integrate with git, putting it under version control. RStudio has a nicer interface to git than shell, but is very limited in what it can do, so you will find yourself occasionally needing to use the shell. Let s go through and make an initial commit of our template files. The workspace/history pane has a tab for Git. We can stage each file by checking the box: you will see a green A next to stage files and folders yellow question marks next to files or folders git doesn t know about yet. RStudio also nicely shows you the difference between files from different commits.

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