Lab 2: Getting Started With Homework

Biostat 203B

This tutorial assumes that you have already installed R, RStudio, and Git on your computer. If not, please refer to the Lab 1.

1 Set up GitHub repo for 203B homework

• On https://github.com/, create a private repository biostat-203b-2024-winter and add Hua-Zhou and TA team (Tomoki-Okuno for Lec 1; jonathanhori and jasenzhang1 for Lec 80) as your collaborators with write permission. This repository is for submitting your 203B homework.

• You can use RStudio to git clone the biostat-203b-2024-winter repository to your local machine: File -> New Project... -> Version Control -> Git -> input Repository URL:, Project directory name: (203b-hw).

• Alternatively, in Terminal (Mac Terminal, Windows Git Bash, or Windows WSL), you can run

git clone [SSH_ADDRESS] ~/203b-hw

to clone your homework repository to a folder called 203b-hw under your home directory on your computer. [SSH_ADDRESS] is obtained by clicking the menu <> Code -> SSH on the repository page on GitHub. Then you can double click the biostat-203b-2024-winter.Rproj file to open the RStudio project.

2 MIMIC Data

Much of homework and exercises are demonstrated on the MIMIC-IV v2.2 data set. Download the data to your computer from here (7.69 GB), and make it available at ~/mimic. For example, you can create a symbolic link by

ln -s /PATH/TO/YOUR/MIMIC_FOLDER ~/mimic

Your homework solution should always read data from ~/mimic. This is critical for TA team to reproduce your homework.

ls -l ~/mimic/

total 24
-rw-r--r--  1 504 rstudio 13332 Jan  5  2023 CHANGELOG.txt
drwxr-xr-x 24 504 rstudio   768 Jan  4 22:18 hosp
drwxr-xr-x 11 504 rstudio   352 Nov 24 19:34 icu
-rw-r--r--  1 504 rstudio  2518 Jan  6  2023 LICENSE.txt
-rw-r--r--  1 504 rstudio  2884 Jan  6  2023 SHA256SUMS.txt

3 Start with homework 1

On your local machine:

• Clone the repository, create develop branch, where your work on solutions.

```{bash}
#| eval: false
# clone the project
git clone git@github.com:[USERNAME]/biostat-203b-2024-winter.git
# enter project folder
cd biostat-203b-2024-winter
# what branches are there?
git branch
# create develop branch
git branch develop
# switch to the develop branch
git checkout develop
# create folder for HW1
mkdir hw1
cd hw1
# let's write solutions
echo "sample solution" > hw1.Rmd
echo "some bug" >> hw1.Rmd
# commit the code
git add hw1.Rmd
git commit -m "start working on problem #1"
# push to remote repo
git push
```

• Submit and tag HW1 solution to the main branch.

```{bash}
#| eval: false
# which branch are we in?
git branch
# change to the main branch
git checkout main
# merge develop branch to main branch
# git pull origin develop 
git merge develop
# push to the remote main branch
git push
# tag version hw1
git tag hw1
git push --tags
```

• RStudio has good Git integration. But practice command line operations also.

4 Homework 1

• Demo Q2, Q3.1, Q3.2, Q5, Q6.