## -----------------------------------------------------------------------------
#| warning: false
library(ggplot2)
study_data <- read.delim("https://raw.githubusercontent.com/IowaBiostat/data-sets/main/diarrhea/diarrhea.txt")


## -----------------------------------------------------------------------------
ggplot(study_data, aes(x=Stool, y = Group)) +
  theme_classic() +
  labs(
    title = "Effect of Bismuth Salicylate", 
    x = "Infant Stool Output (ml/kg)"
  )+
  geom_boxplot(fill = c("grey", "snow2"))


## -----------------------------------------------------------------------------
treat <- subset(study_data, Group == "Treatment")[,-1] # [,-1] removes Group column
control <- subset(study_data, Group == "Control")[,-1] # which is unnecessary after subset


## -----------------------------------------------------------------------------
c(sd(treat), sd(control))


## -----------------------------------------------------------------------------
t.test(treat, control, paired = FALSE, var.equal = TRUE)


## -----------------------------------------------------------------------------
t.test(treat, control, paired = FALSE, var.equal = FALSE)


## -----------------------------------------------------------------------------
#| echo: false
heart <- read.delim('https://raw.githubusercontent.com/IowaBiostat/data-sets/main/infant-heart/infant-heart.txt')


## -----------------------------------------------------------------------------
arrest <- subset(heart, Treatment == "Circulatory arrest")[,-1] 
bypass <- subset(heart, Treatment == "Low-flow bypass")[,-1]

pdi_arrest <- sd(arrest$PDI) |> round(2)
mdi_arrest <- sd(arrest$MDI) |> round(2)
pdi_bypass <- sd(bypass$PDI) |> round(2)
mdi_bypass <- sd(bypass$MDI) |> round(2)


data.frame(
  pdi_arrest = (pdi_arrest),
  pdi_bypass = (pdi_bypass),
  mdi_arrest = (mdi_arrest),
  mdi_bypass = (mdi_bypass)
)


## -----------------------------------------------------------------------------
with(heart, by(PDI, Treatment, sd))
with(heart, by(MDI, Treatment, sd))


## -----------------------------------------------------------------------------
t.test(heart$PDI ~ heart$Treatment, var.equal = T)


## -----------------------------------------------------------------------------
t.test(heart$MDI ~ heart$Treatment, var.equal = T)