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


# Plots
logDiarrhea <- 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)


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

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


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


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


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


# Signed Rank
# 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")