Analysis tutorials

Tutorial scripts to use with LifeCycle analyses.

Setup your environment

We have a few steps to help you setup your environment

• Version control and sharing of analysis
• RStudio-account management

Version-control and sharing of analysis

We want to use version-control to setup a platform where you can share your analysis script and also be able to obtain an older version of the script.

We are using github to do file-versioning and sharing.

1. Create an account on github: join github

2. Create a person access token: create access token

• Follow the steps until 10 (note that the token will only be presented once by Github)
• You will use the token in Step 4 so keep it on your clipboard

3. In R-Studio create a new project

• Create a new project

• Choose "From version control"

• Choose "Git"

• Enter the project url from Github

4. Setup your credentials for the project

• Open up a terminal

• Execute the following command and be aware that you paste you username:token in the github-url. So: "git remote set-url origin https://username:token@github.com/lifecycle-project/analysis-tutorials"

git remote set-url origin https://sidohaakma:[email protected]/lifecycle-project/analysis-tutorials

Tutorials

There are three levels of tutorials we now distinguish.

• beginner
• novice
• advanced (only for experieced R-users)

There are some prerequisites for these tutorials. You have to upload datasets to:

• https://opal1.domain.org
• https://opal2.domain.org

The datasets are speficyfied by in the difficulty level paragraphs.

Beginner tutorials

The beginners tutorials are containing a set of excersizes that are fit for beginning R and DataSHIELD users.

For the beginners-tutorial you need to create a "Project": Tutorials and then create a table called: tutorial_beginner Use these files for the beginners tutorial:

• metadata
• dataset1
• dataset2

First steps in DataSHIELD

Created by Sido Haakma

An age analyses on 2 datasets in the 2 test-opals.

Novice tutorials

If you already have some experience in doing R-analyses you can do these tutorials.

More specific implementation on LifeCycle-framework

Created by Angela Pinot de Moira

For the novices-tutorial you need to create a "Project": Tutorials and then create a table called: tutorial_novice Use these files for the novices tutorial:

• metadata
• dataset

This tutorial includes a more specific anlaysis and datamanipulation implementation on LifeCycle data.

Advanced tutorials

You can attend these tutorials if are certified by Angela or Sido in the LifeCycle project.

Some more exploration on how to use DataSHIELD

Created by Tom Bishop

For the advanced-tutorial you need to create a "Project": Tutorials and then create a table called: tutorial_advanced Use these files for the advanced tutorial:

• metadata
• dataset

This tutorial includes some data manipulation in R and some sample statitics you can perform in R.