## ----style, echo = FALSE, results = 'asis'---------------------------------
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

## ----search----------------------------------------------------------------
search()

## --------------------------------------------------------------------------
library("survival")

## ----eval=FALSE------------------------------------------------------------
#  library(help="survival")
#  ls(2)

## ----eval=FALSE------------------------------------------------------------
#  install.packages("ggplot2", repos="https://cran.r-project.org")

## ----eval=FALSE------------------------------------------------------------
#  BiocInstaller::biocLite("ggplot2")

## ----echo=FALSE------------------------------------------------------------
path <- system.file(package="BiocIntro", "extdata", "BRFSS-subset.csv")
brfss <- read.csv(path)

## ---- eval=FALSE-----------------------------------------------------------
#  path <- file.choose()  # or file.path
#  brfss <- read.csv(path)

## --------------------------------------------------------------------------
brfss$Year <- factor(brfss$Year)

## --------------------------------------------------------------------------
brfss2010Male <- subset(brfss, (Year == 2010) & (Sex == "Male"))
fit <- lm(Weight ~ Height, brfss2010Male)
  
plot(Weight ~ Height, brfss2010Male, main="2010, Males")
abline(fit, lwd=2, col="blue")
points(180, 90, pch=20, cex=3, col="red")

## --------------------------------------------------------------------------
brfssFemale <- subset(brfss, Sex=="Female")

opar = par(mfrow=c(2, 1))     # layout: 2 'rows' and 1 'column'
hist(                         # first panel -- 1990
    brfssFemale[ brfssFemale$Year == 1990, "Weight" ],
    main = "Female, 1990")
hist(                         # second panel -- 2010
    brfssFemale[ brfssFemale$Year == 2010, "Weight" ],
    main = "Female, 2010")
par(opar)                      # restore original layout

## --------------------------------------------------------------------------
library(ggplot2)

## ---- warning=FALSE--------------------------------------------------------
ggplot(brfss2010Male, aes(x=Height, y=Weight)) +
    geom_point() +
    geom_smooth(method="lm")

## ---- warning=FALSE--------------------------------------------------------
plt <- ggplot(brfss2010Male, aes(x=Height, y=Weight)) +
    geom_point() +
    geom_smooth(method="lm")
plt + labs(title = "2010 Male")

## ---- warning=FALSE--------------------------------------------------------
ggplot(brfssFemale, aes(x=Height, y=Weight)) +
    geom_point() + geom_smooth(method="lm") +
    facet_grid(. ~ Year)

## ---- warning=FALSE--------------------------------------------------------
ggplot(brfssFemale, aes(Weight, fill=Year)) +
    geom_density(alpha=.2)