library(tidyverse)
met <- read_csv("https://denvirlab.marshall.edu/BMR617-2021/data/TH-B6-metabolic.csv")
met <- separate(met, MouseID, sep="-", into=c("Strain", "Diet", "ID"))
# Filter for TH Chow:
th_chow <- filter(met, Strain=="TH" & Diet == "Chow")
# Get the cholesterol values from the table:
chol_th_chow <- pull(th_chow, Cholesterol) 
m <- mean(chol_th_chow)
s <- sd(chol_th_chow)
n <- length(chol_th_chow)
conf_level <- 0.95
t_star <- qt((1+conf_level)/2, df=n-1)
conf_int_lower <- m - t_star*s/sqrt(n)
conf_int_upper <- m + t_star*s/sqrt(n)

conf_int <- function(x, conf_level=0.95) {
  m <- mean(x)
  s <- sd(x)
  n <- length(x)
  t_star <- qt((1+conf_level)/2, df=n-1)
  conf_int_lower <- m - t_star*s/sqrt(n)
  conf_int_upper <- m + t_star*s/sqrt(n)
  return(c(conf_int_lower, conf_int_upper))
}
conf_int(chol_th_chow)

met_grouped <- group_by(met, Strain, Diet)
met_summary <- summarize(met_grouped, 
      MeanCholesterol = mean(Cholesterol),
      lowerCI = conf_int(Cholesterol, conf_level=0.95)[[1]],
      upperCI = conf_int(Cholesterol, conf_level=0.95)[[2]])
barplot <- ggplot(met_summary, aes(x=Diet, y=MeanCholesterol, fill=Strain)) +
  geom_bar(stat='identity', position=position_dodge())
ciError <- geom_errorbar(aes(ymin=lowerCI, ymax=upperCI), 
                         position=position_dodge(width=0.9), width=0.2)
barplot + ciError