# NOT RUN {
# The sample data set is an augmented CDC AIDS dataset (ASCII)
# which is used in the examples in the help file.  This dataset is
# described in Kalbfleisch and Lawless (JASA, 1989).
# Here, we have included only children 4 years old and younger.
# We have also added a new field, dethdate, which
# represents a fictitious death date for each patient.  There was
# no recording of death date on the original dataset.  In addition, we have
# added a fictitious viral load reading (copies/ml) for each patient at time of AIDS diagnosis,
# noting viral load was also not part of the original dataset.
#
# All dates are julian with julian=0 being
# January 1, 1960, and julian=14000 being 14000 days beyond
# January 1, 1960 (i.e., May 1, 1998).

library(Hmisc)

cdcaids <- data.frame(
    age=c(4,2,1,1,2,2,2,4,2,1,1,3,2,1,3,2,1,2,4,2,2,1,4,2,4,1,4,2,1,1,3,3,1,3),
    infedate=c(
        7274,7727,7949,8037,7765,8096,8186,7520,8522,8609,8524,8213,8455,8739,
        8034,8646,8886,8549,8068,8682,8612,9007,8461,8888,8096,9192,9107,9001,
        9344,9155,8800,8519,9282,8673),
    diagdate=c(
        8100,8158,8251,8343,8463,8489,8554,8644,8713,8733,8854,8855,8863,8983,
        9035,9037,9132,9164,9186,9221,9224,9252,9274,9404,9405,9433,9434,9470,
        9470,9472,9489,9500,9585,9649),
    diffdate=c(
        826,431,302,306,698,393,368,1124,191,124,330,642,408,244,1001,391,246,
        615,1118,539,612,245,813,516,1309,241,327,469,126,317,689,981,303,976),
    dethdate=c(
        8434,8304,NA,8414,8715,NA,8667,9142,8731,8750,8963,9120,9005,9028,9445,
        9180,9189,9406,9711,9453,9465,9289,9640,9608,10010,9488,9523,9633,9667,
        9547,9755,NA,9686,10084),
    censdate=c(
        NA,NA,8321,NA,NA,8519,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
        NA,NA,NA,NA,NA,NA,NA,NA,NA,10095,NA,NA),
    viralload=c(
        13000,36000,70000,90000,21000,110000,75000,12000,125000,110000,13000,39000,79000,135000,14000,
        42000,123000,20000,12000,18000,16000,140000,16000,58000,11000,120000,85000,31000,24000,115000,
        17000,13100,72000,13500)
)

# cdcaids <- upData(cdcaids,
#                   labels=c(age     ='Age, y', infedate='Date of blood transfusion',
#                            diagdate='Date of AIDS diagnosis',
#                            diffdate='Incubation period (days from HIV to AIDS)',
#                            dethdate='Fictitious date of death',
#                            censdate='Fictitious censoring date',
#                            viralload='Fictitious viral load'))

# contractData <- upData(contractData,
#                   labels=c(age     ='Age, y', infedate='Date of blood transfusion',
#                            diagdate='Date of AIDS diagnosis',
#                            diffdate='Incubation period (days from HIV to AIDS)',
#                            dethdate='Fictitious date of death',
#                            censdate='Fictitious censoring date',
#                            viralload='Fictitious viral load'))



# Note that the style options listed with these
# examples are best suited for output to a postscript file (i.e., using
# the postscript function with horizontal=TRUE) as opposed to a graphical
# window (e.g., motif).


# To produce simple calendar event chart (with internal legend):
# postscript('example1.ps', horizontal=TRUE)
# event.chart(cdcaids,
#             subset.c=c('infedate','diagdate','dethdate','censdate'),
#             x.lab = 'observation dates',
#             y.lab='patients (sorted by AIDS diagnosis date)',
#             titl='AIDS data calendar event chart 1',
#             point.pch=c(1,2,15,0), point.cex=c(1,1,0.8,0.8),
#             legend.plot=TRUE, legend.location='i', legend.cex=1.0,
#             legend.point.text=c('transfusion','AIDS diagnosis','death','censored'),
#             legend.point.at = list(c(7210, 8100), c(35, 27)), legend.bty='o')
#contractData$EndDate <- as.Date(contractData$EndDate)
event.chart(contractData,
            subset.c=c('Name', 'EndDate'),
            x.lab = 'Dates',
            y.lab='Service Provider',
            titl='Contract Dates',
            point.pch=c(1,2,15,0), point.cex=c(1,1,0.8,0.8),
            legend.plot=TRUE, legend.location='i', legend.cex=1.0,
            legend.point.text=c('Start Date','End Date'),
            legend.point.at = list(c(7210, 8100), c(35, 27)), legend.bty='o')





# To produce simple interval event chart (with internal legend):
# postscript('example2.ps', horizontal=TRUE)
# event.chart(cdcaids,
#             subset.c=c('infedate','diagdate','dethdate','censdate'),
#             x.lab = 'time since transfusion (in days)',
#             y.lab='patients (sorted by AIDS diagnosis date)',
#             titl='AIDS data interval event chart 1',
#             point.pch=c(1,2,15,0), point.cex=c(1,1,0.8,0.8),
#             legend.plot=TRUE, legend.location='i', legend.cex=1.0,
#             legend.point.text=c('transfusion','AIDS diagnosis','death','censored'),
#             x.reference='infedate', x.julian=TRUE,
#             legend.bty='o', legend.point.at = list(c(1400, 1950), c(7, -1)))


# To produce simple interval event chart (with internal legend),
# but now with flexible diagdate symbol size based on viral load variable:
# postscript('example2a.ps', horizontal=TRUE)
event.chart(cdcaids,
            subset.c=c('infedate','diagdate','dethdate','censdate'),
            x.lab = 'time since transfusion (in days)',
            y.lab='patients (sorted by AIDS diagnosis date)',
            titl='AIDS data interval event chart 1a, with viral load at diagdate represented',
            point.pch=c(1,2,15,0), point.cex=c(1,1,0.8,0.8),
            point.cex.mult = 0.00002, point.cex.mult.var = 'viralload', extra.points.no.mult = c(1,NA,1,1),
            legend.plot=TRUE, legend.location='i', legend.cex=1.0,
            legend.point.text=c('transfusion','AIDS diagnosis','death','censored'),
            x.reference='infedate', x.julian=TRUE,
            legend.bty='o', legend.point.at = list(c(1400, 1950), c(7, -1)))


# To produce more complicated interval chart which is
# referenced by infection date, and sorted by age and incubation period:
# postscript('example3.ps', horizontal=TRUE)
event.chart(cdcaids,
            subset.c=c('infedate','diagdate','dethdate','censdate'),
            x.lab = 'time since diagnosis of AIDS (in days)',
            y.lab='patients (sorted by age and incubation length)',
            titl='AIDS data interval event chart 2 (sorted by age, incubation)',
            point.pch=c(1,2,15,0), point.cex=c(1,1,0.8,0.8),
            legend.plot=TRUE, legend.location='i',legend.cex=1.0,
            legend.point.text=c('transfusion','AIDS diagnosis','death','censored'),
            x.reference='diagdate', x.julian=TRUE, sort.by=c('age','diffdate'),
            line.by='age', line.lty=c(1,3,2,4), line.lwd=rep(1,4), line.col=rep(1,4),
            legend.bty='o', legend.point.at = list(c(-1350, -800), c(7, -1)),
            legend.line.at = list(c(-1350, -800), c(16, 8)),
            legend.line.text=c('age = 1', '       = 2', '       = 3', '       = 4'))


# To produce the Goldman chart:
# postscript('example4.ps', horizontal=TRUE)
event.chart(cdcaids,
            subset.c=c('infedate','diagdate','dethdate','censdate'),
            x.lab = 'time since transfusion (in days)', y.lab='dates of observation',
            titl='AIDS data Goldman event chart 1',
            y.var = c('infedate'), y.var.type='d', now.line=TRUE, y.jitter=FALSE,
            point.pch=c(1,2,15,0), point.cex=c(1,1,0.8,0.8), mgp = c(3.1,1.6,0),
            legend.plot=TRUE, legend.location='i',legend.cex=1.0,
            legend.point.text=c('transfusion','AIDS diagnosis','death','censored'),
            x.reference='infedate', x.julian=TRUE,
            legend.bty='o', legend.point.at = list(c(1500, 2800), c(9300, 10000)))


# To convert coded time-to-event data, then, draw an event chart:
surv.time <- c(5,6,3,1,2)
cens.ind   <- c(1,0,1,1,0)
surv.data  <- cbind(surv.time,cens.ind)
event.data <- event.convert(surv.data)
event.chart(cbind(rep(0,5),event.data),x.julian=TRUE,x.reference=1)
# }