## ------------------------------------------------------------------------
# Generate 50 values drawn randomly from two different distributions: x is from a normal distribution and y from a uniform.
# Thus, we *know* they should be different
x <- rnorm(50)
y <- runif(30)

# Do x and y come from the same distribution?
ks.test(x, y)

## ------------------------------------------------------------------------
BirdData <- data.frame(
            Tarsus  = c(22.3, 19.7, 20.8, 20.3, 20.8, 21.5, 20.6, 21.5),
            Head    = c(31.2, 30.4, 30.6, 30.3, 30.3, 30.8, 32.5, 31.6),
            Weight  = c(9.5, 13.8, 14.8, 15.2, 15.5, 15.6, 15.6, 15.7),
            Wingcrd = c(59, 55, 53.5, 55, 52.5, 57.5, 53, 55),
            Species = c('A', 'A', 'A', 'A', 'A',  'B', 'B', 'B')
            )

## ---- birdplots, fig.cap = "**Fig.** The relationships between measurements of sparrows"----
par(mfrow = c(2, 2))
plot(BirdData$Tarsus ~ BirdData$Wingcrd)
plot(BirdData$Tarsus ~ BirdData$Head)
plot(BirdData$Tarsus ~ BirdData$Weight)
plot(BirdData$Head ~ BirdData$Wingcrd)

## ------------------------------------------------------------------------
cor(x = BirdData$Tarsus, y = BirdData$Wingcrd, method = 'pearson')

## ------------------------------------------------------------------------
cor.test(x = BirdData$Tarsus, y = BirdData$Wingcrd, method = 'pearson')

## ------------------------------------------------------------------------
cor.test(formula = ~ BirdData$Tarsus + BirdData$Wingcrd)

## ---- fig.cap = "**Fig.** Sparrow Wingcrd as a function of Tarsus length"----
plot(BirdData$Tarsus ~ BirdData$Wingcrd)

## ------------------------------------------------------------------------
m <- lm(BirdData$Tarsus ~ BirdData$Wingcrd)

# or
m <- lm(Tarsus ~ Wingcrd, data = BirdData)

## ------------------------------------------------------------------------
summary(m)

## ------------------------------------------------------------------------
coef(m)

## ------------------------------------------------------------------------
resid(m)

## ---- fig.cap = "**Fig.** Sparrow Wingcrd as a function of Tarsus length, with fitted line"----
plot(BirdData$Tarsus ~ BirdData$Wingcrd)
abline(lm(BirdData$Tarsus ~ BirdData$Wingcrd))

# or
m <- lm(BirdData$Tarsus ~ BirdData$Wingcrd)
abline(m)