---
title: "Biostatistics III in R"
author:
- Code by Andreas Karlsson and Mark Clements
output:
  html_document:
    theme: null
  html_vignette: default
  prettydoc::html_pretty: default
---

# Cox model for cause-specific mortality for melanoma (all stages) #


Use Cox regression to model the cause-specific survival of patients with skin melanoma (including all stages).

-----------


```{r setup, cache=FALSE, message=FALSE, echo=FALSE}
library('knitr')
read_chunk('../q12.R')
opts_chunk$set(cache=FALSE)
```

You may have to install the required packages the first time you use them. You can install a package by `install.packages("package_of_interest")` for each package you require.

```{r loadDependencies, message=FALSE}
```
Load the melanoma data and explore it.

```{r loadPreprocess, results='hide'}
```

## (a) ## 
First fit the model with sex as the only explanatory variable. Does there appear to be a difference in survival between males and females?


```{r 12.a, warning=FALSE, message=FALSE, results='hide'}
```

## (b) ## 
Is the effect of sex confounded by other factors (e.g. age, stage, subsite, period)? After controlling for potential confounders, does there still appear to a difference in survival between males and females?

```{r 12.b, warning=FALSE, message=FALSE, results='hide'}
```

## (c) ## 
Consider the hypothesis that there exists a class of melanomas where female sex hormones play a large role in the etiology. These hormone related cancers are diagnosed primarily in women and are, on average, less aggressive (i.e., prognosis is good). If such a hypothesis were true we might expect the effect of sex to be modified by age at diagnosis (e.g., pre versus post menopausal). Test whether this is the case.

```{r 12.c, warning=FALSE, message=FALSE, results='hide'}
```

## (d) ## 
Decide on a ‘most appropriate’ model for these data. Be sure to evaluate the proportional hazards assumption.


```{r 12.d.i, warning=FALSE, message=FALSE, results='hide'}
```

```{r 12.d.ii, warning=FALSE, message=FALSE, results='hide'}
```

```{r 12.d.iii, warning=FALSE, message=FALSE, results='hide'}
```
