Figures.Rmd

---
title: "Figures"
author: "EE Holmes"
output:
  html_document:
    fig_caption: yes
---

```{r include=FALSE}
# include = FALSE means don't show code or any output (like warnings)
# It is good to set up any knitr options that you want at the top of all your Rmds
knitr::opts_chunk$set(echo = TRUE)
```

```{r load_data, echo=FALSE}
load("landings.RData")
landings$log.metric.tons = log(landings$metric.tons)
landings = subset(landings, Year <= 1989)
```



```{r poly.plot, fig.height=4, fig.width=8, fig.align="center"}
par(mfrow=c(1,4))
tt <- seq(-5,5,.01)
plot(tt,type="l",ylab="",xlab="")
title("1st order")
plot(tt^2,type="l",ylab="",xlab="")
title("2nd order")
plot(tt^3-3*tt^2-tt+3,ylim=c(-100,50),type="l",ylab="",xlab="")
title("3rd order")
plot(tt^4+2*tt^3-12*tt^2-2*tt+6,ylim=c(-100,100),type="l",ylab="",xlab="")
title("4th order")
```

Specify `echo=FALSE` to hide the figure code.  Set `message=FALSE` and `warning=FALSE` to suppress package loading messages.

```{r fig.stationarity2, fig.height = 4, fig.width = 8, fig.align = "center", echo=FALSE, warning=FALSE, message=FALSE, fig.cap="test"}
require(ggplot2)
require(reshape2)
require(gridExtra)
TT <- 100
theta <- 0.8
nsim <- 10
ar1 <- as.vector(arima.sim(TT, model=list(ar=theta)))
dat <- data.frame(t=1:TT, y=ar1)
p1 <- ggplot(dat, aes(x=t, y=y)) + geom_line() + 
  ggtitle("AR-1") + xlab("") + ylab("value")
ys <- matrix(0,TT,nsim)
for(i in 1:nsim) ys[,i]=as.vector(arima.sim(TT, model=list(ar=theta)))
ys <- data.frame(ys)
ys$id <- 1:TT

ys2 <- melt(ys, id.var="id")
p2 <- ggplot(ys2, aes(x=id,y=value,group=variable)) +
  geom_line() + xlab("") + ylab("value") +
  ggtitle("The variance of an AR-1 process is steady")
grid.arrange(p1, p2, ncol = 1)
```

You can include figure legends if your yaml has
```
output:
  html_document:
    fig_caption: yes

```

```{r poly.plot2, fig.align="center", fig.cap="Here is a 4th order polynomial.", echo=FALSE}
tt <- seq(-5,5,.01)
plot(tt^4+2*tt^3-12*tt^2-2*tt+6,ylim=c(-100,100),type="l",ylab="",xlab="")
```