IDEAS2020workshop.rmd

---
title: "IDEAS Comp Bio workshop 2020"
author: "Lambodhar Damodaran"
date: "5/19/2020"
output: pdf_document
---

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


## Libraries needed



```{r}
library(lubridate)
library(ggplot2)
library(plotly)
```



## R Markdown

Reading in data file for mers and manipulating to determine days since onset of epidemic, reformmating date information. 

```{r}
mers <- read.csv('cases.csv')
mers$hospitalized[890] <- c('2015-02-20')
mers <- mers[-471,]
mers$onset2 <- ymd(mers$onset)
mers$hospitalized2 <- ymd(mers$hospitalized)
class(mers$onset2)

day0 <- min(na.omit(mers$onset2))
mers$epi.day <- as.numeric(mers$onset2 - day0)
```

##Plots data

Plotting MERS epidemnic day vs case count using ggplot. 

```{r}
ggplot(data=mers) +
  geom_bar(mapping = aes(x=epi.day)) +
  labs(x='Epidemic day', y='Case count', title = 'Global MERS case count by dat of onset', caption = 'Data from Rambaut - MERS')


```


## Interactive plotly plot


```{r}

epi.curve <- ggplot(data=mers) +
  geom_bar(mapping=aes(x=epi.day)) +
  labs(x='Epidemic day', y='Case count', title='Global MERS case count by onset date', caption = 'Data from Rambaut - MERS')

ggplotly(epi.curve)
```