require(Hmisc)
set.seed(2)
d <- expand.grid(major=c('Alabama', 'Alaska', 'Arkansas',
                         'Arizona', 'Nevada'),
                 minor=c('East', 'West'),
                 group=c('Female', 'Male'),
                 city=0:2)
n <- nrow(d)
# d$x <- (1 : nrow(d)) + runif(n)
d$num <- round(100*runif(n))
d$denom <- d$num + round(100*runif(n))
d$x <- d$num / d$denom
d

with(d,
     dotchartpl(x, major, minor, group, city, big=city==0, num=num, denom=denom)
     )

## Same without city, compute Famale - Male differences and conf. intervals
## Within major groups sort in descending order of differences, show
## differences with color of Female if positive, Male if negative,
## add layer with horizontal bar centered at the difference and with
## width equal to half-width of confidence interval
d <- subset(d, city==0)
i <- with(d, order(major, minor, group))
xless(d[i, ])
with(d,
     dotchartpl(x, major, minor, group, refgroup='Male', num=num, denom=denom,
                  xlim=c(0,1))
     )


# Original source of aeanonym: HH package
# aeanonym <- read.table(hh("datasets/aedotplot.dat"), header=TRUE, sep=",")
# Modified to remove denominators from data and to generate raw data
# (one record per event per subject)

ae <-
    structure(list(RAND = structure(c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 
                                      2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 
                                      2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 
                                      2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 
                                      2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L), .Label = c("a", 
                                                                                              "b"), class = "factor"), PREF = structure(c(12L, 12L, 
                                                                                                                                          18L, 18L, 26L, 26L, 33L, 33L, 5L, 5L, 27L, 27L, 6L, 6L, 15L, 
                                                                                                                                          15L, 22L, 22L, 23L, 23L, 31L, 31L, 17L, 17L, 2L, 2L, 3L, 3L, 
                                                                                                                                          13L, 13L, 25L, 25L, 28L, 28L, 14L, 14L, 4L, 4L, 8L, 8L, 19L, 
                                                                                                                                          19L, 21L, 21L, 29L, 29L, 10L, 10L, 20L, 20L, 16L, 16L, 32L, 32L, 
                                                                                                                                          11L, 11L, 1L, 1L, 30L, 30L, 24L, 24L, 9L, 9L, 7L, 7L),
                                                                                                                                        .Label = tolower(c("ABDOMINAL PAIN", 
                                                                                                                                                           "ANOREXIA", "ARTHRALGIA", "BACK PAIN", "BRONCHITIS", "CHEST PAIN", 
                                                                                                                                                           "CHRONIC OBSTRUCTIVE AIRWAY", "COUGHING", "DIARRHEA", "DIZZINESS", 
                                                                                                                                                           "DYSPEPSIA", "DYSPNEA", "FATIGUE", "FLATULENCE", "GASTROESOPHAGEAL REFLUX", 
                                                                                                                                                           "HEADACHE", "HEMATURIA", "HYPERKALEMIA", "INFECTION VIRAL", "INJURY", 
                                                                                                                                                           "INSOMNIA", "MELENA", "MYALGIA", "NAUSEA", "PAIN", "RASH", "RESPIRATORY DISORDER", 
                                                                                                                                                           "RHINITIS", "SINUSITIS", "UPPER RESP TRACT INFECTION", "URINARY TRACT INFECTION", 
                                                                                                                                                           "VOMITING", "WEIGHT DECREASE")), class = "factor"), SAE = c(15L, 
                                                                                                                                                                                                                       9L, 4L, 9L, 4L, 9L, 2L, 9L, 8L, 11L, 4L, 11L, 9L, 12L, 5L, 12L, 
                                                                                                                                                                                                                       7L, 12L, 6L, 12L, 6L, 12L, 2L, 14L, 2L, 15L, 1L, 15L, 4L, 16L, 
                                                                                                                                                                                                                       4L, 17L, 11L, 17L, 6L, 20L, 10L, 23L, 13L, 26L, 12L, 26L, 4L, 
                                                                                                                                                                                                                       26L, 13L, 28L, 9L, 29L, 12L, 30L, 14L, 36L, 6L, 37L, 8L, 42L, 
                                                                                                                                                                                                                       20L, 61L, 33L, 68L, 10L, 82L, 23L, 90L, 76L, 95L)), .Names = c("RAND", 
                                                                                                                                                                                                                                                                                      "PREF", "SAE"), class = "data.frame", row.names = c(NA, 
                                                                                                                                                                                                                                                                                                                                          -66L))

ae$n <- ifelse(ae$RAND == 'a', 212, 188)
ae$p <- ae$SAE / ae$n
# ae <- subset(ae, p >= 0.05)
with(ae, dotchartpl(p, num=SAE, denom=n, minor=PREF, group=RAND, refgroup='a'))


n <- 500
set.seed(1)
d <- data.frame(
  race         = sample(c('Asian', 'Black/AA', 'White'), n, TRUE),
  sex          = sample(c('Female', 'Male'), n, TRUE),
  treat        = sample(c('A', 'B'), n, TRUE),
  smoking      = sample(c('Smoker', 'Non-smoker'), n, TRUE),
  hypertension = sample(c('Hypertensive', 'Non-Hypertensive'), n, TRUE),
  region       = sample(c('North America','Europe','South America',
                          'Europe', 'Asia', 'Central America'), n, TRUE))

d <- upData(d, labels=c(race='Race', sex='Sex'))

dm <- addMarginal(d, region)
s <- summaryP(race + sex + smoking + hypertension ~
                region + treat,  data=dm)

## add exclude1=FALSE to include female category
ggplot(s, groups='treat', exclude1=TRUE, abblen=12)
ggplot(s, groups='region')

s$region <- ifelse(s$region == 'All', 'All Regions', as.character(s$region))

with(s, 
 dotchartpl(freq / denom, major=var, minor=val, group=treat, mult=region,
            big=region == 'All Regions', num=freq, denom=denom)
)

s2 <- s[- attr(s, 'rows.to.exclude1'), ]
with(s2, 
     dotchartpl(freq / denom, major=var, minor=val, group=treat, mult=region,
                big=region == 'All Regions', num=freq, denom=denom)
)




