# Read in Data
diarrhea <- read.delim("http://myweb.uiowa.edu/pbreheny/data/diarrhea.txt")
boxplot(diarrhea$Stool~diarrhea$Group, main = "Effect of Bismuth Salicylate", horizontal = T, col = c("lightblue", "pink"))


# Plots
diarrhea$logStool <- log(diarrhea$Stool)
library(ggplot2)

#Original
ggplot(diarrhea, aes(x = Stool)) + geom_histogram(fill = "tomato3", color = "black", bins = 20) + facet_wrap(~Group)

#Log-transformed
ggplot(diarrhea, aes(x = log(Stool))) + geom_histogram(fill = "tomato3", color = "black", bins = 20) + facet_wrap(~Group)


# 
# Original
t.test(diarrhea$Stool~diarrhea$Group,var.equal=TRUE)

# log-transformed
t.test(diarrhea$logStool~diarrhea$Group,var.equal=TRUE)


# Confidence Intervals
logCI <- t.test(diarrhea$logStool~diarrhea$Group,var.equal=TRUE)$conf.int
exp(logCI)


# 
by(diarrhea$logStool, diarrhea$Group, mean)


# results = "hide"
estimate <- 5.2124-4.8706
exp(estimate)


# 
# Rank-Sum Test
wilcox.test(diarrhea$Stool~diarrhea$Group)


# 
# Signed Rank Test
oatbran <- read.delim("http://myweb.uiowa.edu/pbreheny/data/oatbran.txt")
wilcox.test(oatbran$CornFlakes, oatbran$OatBran, paired=TRUE)

# For comparison, in case you don't remember:
t.test(oatbran$CornFlakes, oatbran$OatBran, paired=TRUE)


# Nhanes Data Plot
nhanes <- read.delim("http://myweb.uiowa.edu/pbreheny/data/nhanes-am.txt")
plot(nhanes$Weight~nhanes$Height)


# Spearmans Correlation
## #Spearman's Rank Correlation
## cor.test(nhanes$Height, nhanes$Weight, method = "spearman")
## 
## #For comparison, here's what we got using Pearson's correlation:
## cor.test(nhanes$Height, nhanes$Weight, method = "pearson")


# 
set.seed(58008)
icecream <- as.data.frame(matrix(c(rep("A", 40), rep("B", 60)), nrow = 100))
colnames(icecream) <- "group"
var1 <- rlnorm(40, meanlog = 0, sdlog = 1)
var2 <- rgamma(60, shape = 1, rate = 0.5)

icecream$cups <- c(var1, var2)

# Normal data: we observe it appears right-skewed
ggplot(icecream, aes(x = cups)) + geom_histogram(fill = "pink", color = "black", bins = 20) + facet_wrap(~group)


# 
fibrosis <- read.delim("https://s3.amazonaws.com/pbreheny-data-sets/cystic-fibrosis.txt")


# 
nhanes_woman <- read.delim("https://s3.amazonaws.com/pbreheny-data-sets/nhanes-aw.txt")