## ----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")))

## ----brfss-aggregate-formula-----------------------------------------------
aggregate(Weight ~ Year + Sex, brfss, mean)  # same, but more informative
aggregate(. ~ Year + Sex, brfss, mean)       # all variables

## ----t-test-1990-----------------------------------------------------------
brfss_1990 = brfss[brfss$Year == 1990,]
t.test(Weight ~ Sex, brfss_1990)
t.test(Weight ~ Sex, brfss, subset = Year == 1990)

## ----brfss-boxplot, fig.width=5, fig.height=5------------------------------
boxplot(Weight ~ Year, brfss, subset = Sex == "Male",
        main="Males")

## ----ALL-subset-NA---------------------------------------------------------
idx <- pdata$sex == "F" & pdata$age > 40
table(idx, useNA="ifany")
dim(pdata[idx,])           # WARNING: 'NA' rows introduced
tail(pdata[idx,])
dim(subset(pdata, idx))    # BETTER: no NA rows
dim(subset(pdata, (sex == "F") & (age > 40)))  # alternative
tail(subset(pdata,idx))

## robust `[`: exclude NA values
dim(pdata[idx & !is.na(idx),])

## ----ALL-BCR/ABL-subset----------------------------------------------------
bcrabl <- subset(pdata, mol.biol %in% c("BCR/ABL", "NEG"))