Thank you for your interest in the GenRe-Mekong’s Introduction to Genetic Report Card Data Analysis and Genetic Epidemiology Mapping training workshop. The aim of this workshop is to train participants to make full use of the Genetic Report Cards (GRC) data, perform informative analyses and create maps for the benefit of public health in the Greater Mekong Subregion countries.
To make the most of our time during the workshop, we would like you to install the required software and follow all the instructions below before attending the workshop. Please reserve about 1 hour of time to complete all the steps.
If you encounter problems with any of the below steps, please reach out to tess@tropmedres.ac and we will help you on your way.
Table of contents
- I don’t have R & R studio on my laptop
- I already have R & R studio on my laptop
- Install R tools (only for Windows users)
- Save workshop dataset and R notebook
- Load R notebook in R studio, and follow instructions
I don’t have R & R studio on my laptop
Install R
1. Download R
If you use Windows, click on the following link: https://cran.rstudio.com/bin/windows/base/R-4.2.3-win.exe
If you use macOS, click on the following link:
https://cran.rstudio.com/bin/macosx/big-sur-arm64/base/R-4.2.3-arm64.pkg
This will start the download of the latest R version (4.2.3)
2. Follow installation instructions
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Install R studio
1. Download Rstudio
If you use Windows 10/11, click on the following link: https://download1.rstudio.org/electron/windows/RStudio-2023.03.0-386.exe, If you use macOS 11+, click on the following link: https://download1.rstudio.org/electron/macos/RStudio-2023.03.0-386.dmg
This will start the download of the latest R studio version (0.3.0). --Follow instructions of ‘RStudio Setup’
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Open R studio
- Go to the location where you saved R studio (for example: C:/Program Files/RStudio), and click on the R studio icon
- Choose to use R-4.2.3 by clicking on the following boxes:
R studio will now open, and look similar to the example below. R studio is now ready for use.
I already have R & R studio on my laptop
Update R
1. Open R studio
Look at your console and check if version 4.2.3 is currently in use,
2. If this is not the case, go to the upper task bar —> select ‘Tools’ —> ‘Global Options’. Subsequently for ‘R version’ click ‘Change’, and select R-4.2.3 if available (see below)
3. If R-4.2.3 is not available, then click on the following link to install this version:
For Windows: https://cran.rstudio.com/bin/windows/base/R-4.2.3-win.exe
For macOS 11 (Big Sur) and higher:
https://cran.rstudio.com/bin/macosx/big-sur-arm64/base/R-4.2.3-arm64.pkg
For macOS 10.13 (High Sierra) and higher:
https://cran.r-project.org/bin/macosx/base/R-4.2.3.pkg
This will start the download of the latest R version (4.2.3)
Subsequently, follow installation instructions.
4. Repeat step 2
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Update R studio
- Go to the upper task bar —> select ‘Help’ —> select ‘Check for Updates’. You might receive a similar message:
Click on ‘Remind Later’. And click on the following link: https://download1.rstudio.org/electron/windows/RStudio-2023.03.0-386.exe
Subsequently, follow installation instructions.
Install R tools (only for Windows users)
1. Several of the R-packages you will be installing are dependent on R tools, which is a set of programs that is required on Windows to build R packages from source.
Click on the following link: https://cran.r-project.org/bin/windows/Rtools/rtools42/files/rtools42-5355-5357.exe, and follow installation instructions
(It is recommended to use the defaults, including the default installation location of C:\rtools42)
Note: the installation takes several minutes to complete
Mac-specific note: an equivalent of R tools called ‘xcode-select’ will be installed during the next step. Instructions are included in the R notebook.
Save workshop dataset and R notebook
1. Create a folder in your Data (D:) folder, named grcmalaria-workshop (for example: “D:\grcmalaria-workshop”)
Mac-specific note: folder structure is organised differently on macOS systems. Therefore we suggest you create a folder named grcmalaria-workshop under Documents, for example: “/Users/[name of user]/Documents/grcmalaria-workshop/”
2. Save the .zip file containing i) training dataset and ii) R notebook in this folder
3. Extract the files by:
- right click on ‘pre-workshop-preparation-files.zip’ —> Extract all
- select the destination folder where you would like the files to be saved, preferably “D:\grcmalaria-workshop” or for Mac users “/Users/[name of user]/Documents/grcmalaria-workshop/”
Load R notebook in R studio, and follow instructions
Open the ‘Pre-workshop-instructions-grcMalaria-0.4.Rmd’ in RStudio and follow the instructions on the notebook
The tutorial clip below explained how to load the R notebook in R studio, and take you through all the steps in the notebook:
Note: you can watch this video on YouTube with timestamps (by clicking the “YouTube” logo on the video).