---
title: "In-semester Exam"
output:
  html_document:
    code_folding: show
    css: null
    fig_caption: yes
    number_sections: no
    self_contained: yes
    theme: spacelab
    toc: yes
    toc_depth: 3
    toc_float: yes
subtitle: "Example question"
editor_options:
  chunk_output_type: console
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,tidy=TRUE)
show_q = TRUE
show_s = FALSE
```


## SID:

# Instructions

- The exam is expected to run for **1 hour and 50 minutes**. 
- You will additionally be given 5 minutes to download your Rmd file off Canvas and 5 minutes to submit your html file to Canvas.
- The exam will become **active on Canvas at 4pm** at which point you can begin downloading the Rmd file. 
- You should submit your html file on Canvas **at 5:55pm**. Submissions after 6pm will incur a **5\% penalty** increasing every 5 minutes.
- Use the pre-filled rmarkdown file from **Canvas** to help arrange your answers. You are welcome to use or ignore the code chunks I have inserted or add additional ones.
- I recommend that you knit your file every 20-30 minutes to ensure it knits. If you get to 1:55 and **your file won't knit, do not stress**, just submit your Rmd file.
- There are 3 questions. The first is worth $40\%$, the second and third are worth $30\%$ each.
- The exam is 'open computer'. You can use all your notes, google and appropriate help websites. You are not allowed to communicate with others.
- Academic integrity is a core value of the University of Sydney. We expect you to be familiar with the policies and codes covering academic honesty and conduct at the University. You should be aware that The University of Sydney does not tolerate any form of breach or academic dishonesty <https://www.sydney.edu.au/students/academic-dishonesty.html>. 

\clearpage

\clearpage

# Question 1 - HIV (40% of total mark)



```{r echo=TRUE}

HIV = read.csv('https://wimr-genomics.vip.sydney.edu.au/AMED3002/data/HIV.csv')
```


## Part 1

a. 

**Answer:** 

```{r}

```


b. 

**Answer:** 

```{r}

```


c. 

**Answer:** 

```{r}

```



## Part 2



d. 

**Answer:** 

e. 

**Answer:** 

```{r}

```


f.

**Answer:** 

g. 

**Answer:** 

h. 

**Answer:** 

i. 

```{r}

```


j. 

```{r}

```


k. 

**Answer:** 

l. 

**Answer:** 

```{r}

```



## Part 3


m. 

```{r}

```


n. 

```{r}

```


o. 

**Answer:** 

```{r}

```


p. 

```{r}

```


q. 

**Answer:** 

r. 

**Answer:** 

```{r}

```


s. 

**Answer:** 

