## comparing continuous distributions by group

library(lattice)
lattice.options(default.theme = "col.whitebg")

coast <- read.csv(url("http://www.stat.wisc.edu/~deepayan/SIBS2005/datasets/COAST/coast.csv"))



bwplot(factor(sex) ~ (il5.1yr / il5.cb) + (il10.1yr / il10.cb) + (il13.1yr / il13.cb) + (ifng.1yr / ifng.cb),
       data = coast, outer = TRUE, scales = list(x = list(log = 2)),
       layout = c(1, 4),
       xlab = "Increase in Cytokine concentration")


bwplot(factor(sex) ~ (il5.1yr / il5.cb) + (il10.1yr / il10.cb) + (il13.1yr / il13.cb) + (ifng.1yr / ifng.cb),
       data = coast, outer = TRUE, scales = list(x = list(log = 2)),
       layout = c(2, 2), panel = panel.violin,
       xlab = "Increase in Cytokine concentration")


trellis.par.set(reference.line = list(col = 'black'))



print(bwplot(factor(sex) ~ log(ifng.1yr / ifng.cb), data = coast,
             xlab = "Increase in Cytokine concentration"),
      position = c(0, 0.7, 1, 1), more = TRUE)


print(qq(factor(sex) ~ log(ifng.1yr / ifng.cb), data = coast,
         f.value = function(n) c(0, 0.25, 0.5, 0.75, 1),
         aspect = 1),
      position = c(0, 0, 1, 0.7))



qq(factor(sex) ~ log(ifng.1yr / ifng.cb), data = coast, aspect = 1)

tmd(qq(factor(sex) ~ log(ifng.1yr / ifng.cb), data = coast, aspect = 1))



bwplot(factor(wheeze) ~ (il5.1yr / il5.cb) + (il10.1yr / il10.cb) + (il13.1yr / il13.cb) + (ifng.1yr / ifng.cb),
       data = coast, outer = TRUE, scales = list(x = list(log = 2)),
       layout = c(1, 4),
       xlab = "Increase in Cytokine concentration")



print(bwplot(factor(wheeze) ~ log(ifng.1yr / ifng.cb), data = coast,
             xlab = "Increase in Cytokine concentration"),
      position = c(0, 0.7, 1, 1), more = TRUE)


print(qq(factor(wheeze) ~ log(ifng.1yr / ifng.cb), data = coast,
         ##f.value = function(n) c(0, 0.25, 0.5, 0.75, 1),
         aspect = 1),
      position = c(0, 0, 1, 0.7))



qq(factor(wheeze) ~ log(ifng.1yr / ifng.cb), data = coast, aspect = 1)

tmd(qq(factor(wheeze) ~ log(ifng.1yr / ifng.cb), data = coast, aspect = 1))

tmd(qq(factor(cat | dog) ~ log(ifng.1yr / ifng.cb), data = coast, aspect = 1))



## lung data

lung <-
    read.table(url("http://www.stat.wisc.edu/~deepayan/SIBS2005/datasets/LUNG/lung.txt"),
               header = TRUE)

qq(factor(treat) ~ age, data = lung, aspect = 1)

bwplot(factor(treat) ~ age, data = lung, aspect = 1)