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#-->> BEGIN general summary and plotting routines for the NADA package
## Generics
setGeneric("censummary",
function(obs, censored, groups) standardGeneric("censummary"))
## Classes
setClass("censummary", "list")
## Methods
setMethod("censummary",
signature(obs="numeric", censored="logical", groups="missing"),
function (obs, censored, groups)
{
ret = cohn(obs, censored)
ret$n = length(obs)
ret$n.cen = length(obs[censored])
props = c(ret$n, ret$n.cen, pctCen(obs, censored), min(obs), max(obs))
names(props) = c("n", "n.cen", "pct.cen", "min", "max")
limits = data.frame(ret$limit, ret$C, ret$A, ret$P)
colnames(limits) = c("limit", "n", "uncen", "pexceed")
return(new("censummary", list(all=props, limits=limits)))
})
setMethod("censummary",
signature(obs="numeric", censored="logical", groups="factor"),
function (obs, censored, groups)
{
ret = list()
for (i in levels(groups))
{
x = obs[groups == i]
xc = censored[groups == i]
ret[[i]] = censummary(x, xc)
names(ret[i]) = i
}
new("NADAList", ret)
})
setMethod("censummary",
signature(obs="numeric", censored="logical", groups="numeric"),
function (obs, censored, groups)
{
censummary(obs, censored, as.factor(groups))
})
setMethod("show", signature("censummary"), function(object)
{
for (i in names(object))
{
cat(i, ":\n", sep="")
print(object[[i]])
cat("\n")
}
})
censtats =
function(obs, censored)
{
skm = cenfit(obs, censored)
sros = cenros(obs, censored)
smle = cenmle(obs, censored)
med = c(median(skm), median(sros), median(smle))
sd = c(sd(skm), sd(sros), sd(smle)[1])
mean = c(mean(skm)[1], mean(sros), mean(smle)[1])
len = c(length(obs), length(which(censored == T)), pctCen(obs, censored))
names(len) = c("n", "n.cen", "pct.cen")
print(len)
data.frame(median=med, mean=mean, sd=sd, row.names=c("K-M", "ROS", "MLE"))
}
## BEGIN general plots routines
# Dennis' censored boxplots
cenboxplot =
function(obs, cen, group, log=TRUE, range=0, ...)
{
if (log) log="y"
else log=""
if (missing(group))
ret = boxplot(cenros(obs, cen), log=log, range=range, ...)
else
{
modeled = numeric()
groups = character()
for (i in levels(as.factor(group)))
{
mod = suppressWarnings(
cenros(obs[group == i], cen[group == i])$modeled)
grp = rep(i, length(mod))
modeled = c(modeled, mod)
groups = c(groups, grp)
}
boxplot(modeled~as.factor(groups), log=log, range=range, ...)
ret = data.frame(ros.model=modeled, group=groups)
}
# Draw horiz line at max censored value
abline(h=max(obs[cen]))
invisible(ret)
}
# Dennis' censored xy plots -- need to fix this
cenxyplot =
function (x, xcen, y, ycen, log="", lty="dashed", ...)
{
plot(x, y, log = log, type = "n", ...)
points(x[!ycen], y[!ycen], ...)
x0 = x1 = x[ycen]
y0 = rep(cenpar.usr(log)[3], length(x[ycen]))
y1 = y[ycen]
segments(x0, y0, x1, y1, lty=lty, ...)
}
## END general plots routines
#-->> END general summary and plotting routines for the NADA package
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