---
title: "STAT588/BIOL588 Homework Template"
date: "`r Sys.Date()`"
author: John Doe 
output: pdf_document
---
```{r setup, include=FALSE, echo=FALSE}
knitr::opts_chunk$set( warning = FALSE, message=FALSE,
                       fig.height = 4, fig.width = 8)
```

#Problem 1 
Remember to say something to comment on the findings in your analysis. 

```{r faithful and iris data}
data(faithful)
data(iris)

##histograms for faithful and iris
par(mfrow=c(1,2))
Hmisc::hist.data.frame(faithful,freq=FALSE)
plot(faithful$eruptions, faithful$waiting, pch=16, main="Old Faithful", xlab="eruption time", ylab="waiting time")
Hmisc::hist.data.frame(iris[,-5],freq=FALSE)
attach(iris)
plot(Sepal.Length, Petal.Length, col=Species)
##boxplots for faithful and iris
par(mfrow=c(1,2))
boxplot(faithful)
boxplot(iris[,-5])
```

##Problem 2
Make a table here. 
```{r Table}
library(knitr)
mat<-matrix(1:6, nrow=3)
rownames(mat)<-c("A", "B", "C")
colnames(mat)<-c("n=10", "n=20")
kable(mat, caption="A table")
```

```{r O-ring}
x<-c(0,1,0,NA,0,0,0,0,0,1,1,1,0,0,3,0,0,0,0,0,2,0,1)
table(x[!is.na(x)])
mean(x[!is.na(x)])
```

###Problem 3 

```{r, fig.height=6, fig.width=6}
library(viridis)
image(volcano, col=viridis(200))
````

```{r, fig.height=6, fig.width=6}
library(viridis)
image(volcano, col=viridis(200, option="A"))
````

#### Getting R code from .Rmd file 
Extract R code using purl function
```{r Extract R code, eval=FALSE}
library(knitr)
purl("Stat588_HWtemplate.Rmd")
```