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

# Exercise 6. Diet data: tabulating incidence rates and modelling with Poisson regression #

```{r setup, cache=FALSE, message=FALSE, echo=FALSE}
library('knitr')
read_chunk('../q6.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 diet data using time-on-study as the timescale.

```{r loadPreprocess}
```

## (a) ##

```{r 6a_ir,  message=FALSE}
```

We see that individuals with a high energy intake have a lower
        CHD incidence rate. The estimated crude incidence rate ratio
        is 0.52 (95% CI: 0.27, 0.97).

## (b) ##

```{r 6b_ir}
```

The point estimate for the IRR calculated by the Poisson regression is the same as the
        IRR calculated in 6(a). A theoretical observation: if we
        consider the data as being cross-classified solely by `hieng` then
        the Poisson regression model with one parameter is a saturated
        model so the IRR estimated from the model will be identical to
        the ‘observed’ IRR. That is, the model is a perfect fit.

## (c) ##

```{r 6c_energyDist,  message=FALSE}
```

The histogram  gives us an idea of
        the distribution of energy intake. We can also tabulate moments
        and percentiles of the distribution.

## (d) ##

```{r 6d_engCat}
```

## (e) ##


```{r 6e_irEng}
```

We see that the CHD incidence rate decreases as the level of
        total energy intake increases.

## (f) ##


```{r 6f_irEng}
```

## (g) ##

```{r 6g_irEng}
```

## (h) ##

```{r 6h,  message=FALSE}
```

Level 1 of the categorized total energy is the
        reference category. The estimated rate ratio comparing level 2
        to level 1 is 0.6452 and the estimated rate ratio comparing
        level 3 to level 1 is 0.2886.


## (i) ##


```{r 6i,  message=FALSE}
```

Now use level 2 as the reference (by omitting X2 but including
        X1 and X3). The estimated rate ratio comparing level 1 to level
        2 is 1.5498 and the estimated rate ratio comparing level 3 to
        level 2 is 0.4473.

## (j) ##

```{r 6j,  message=FALSE}
```

The estimates are identical (as we would hope) when we have
        R create indicator variables for us.

## (k) ##

Somehow (there are many different alternatives) you’ll need to
        calculate the total number of events and the total person-time
        at risk and then calculate the incidence rate
        as events/person-time. For example,

```{r 6k}
```

The estimated incidence rate is 0.00999 events per person-year.
