report.Rmd

---
title: "Example report"
subtitle: 'DRAFT'
author: "Name"
date: "`r format(Sys.time(), '%Y-%m-%d')`"
fontsize: 12pt
output:
  pdf_document:
    fig_caption: yes
    highlight: tango
    latex_engine: xelatex
  word_document:
    fig_caption: true
  html_document:
    df_print: paged
header-includes: \usepackage{fancyhdr}
mainfont: Arial
geometry: margin=.7in
papersize: a4
always_allow_html: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(deSolve)
library(ggplot2)

source('functions.R')
pp <- readxl::read_excel('parameters.xlsx', sheet = 'parameters')
values <- as.list(pp$Value)
names(values) <- pp$Code
```

```{r run, echo = FALSE}
# Run models

sir_out <- run_model(sir)
sis_out <- run_model(sis)
out <- data.frame(rbind(cbind(sir_out, model = 'SIR')
                        , cbind(sis_out, model = 'SIS')
))
```

# Model functions

```{r show, echo = TRUE}

# SIR model definition
sir

# SIS model definition
sis

# Function to run models
run_model

```

## Parameter Table

```{r table, echo=FALSE, include = TRUE}
knitr::kable(pp[, -ncol(pp)])
```

## Example Plot

```{r plot, echo=FALSE}
(ggplot(out)
 + aes(x = time, y = I, color = model)
 + geom_line(size = 1.5)
 + xlab('Time (in disease generations)')
 + ylab('Proportion of the population infected')
 + theme_bw()
)
```