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## ---- echo = TRUE, fig.width = 7, fig.height = 7-------------------------
require("ggplot2")
huron <- data.frame(year = 1875:1972, level = as.vector(LakeHuron))
h <- ggplot(huron, aes(year))
h + RcmdrPlugin.KMggplot2::geom_stepribbon(
aes(ymin = level - 1, ymax = level + 1),
fill = "grey70"
) +
geom_step(aes(y = level))
h + geom_ribbon(
aes(ymin = level - 1, ymax = level + 1),
fill = "grey70"
) +
geom_line(aes(y = level))
data(dataKm, package = "RcmdrPlugin.KMggplot2")
.df <- na.omit(data.frame(x = dataKm$time, y = dataKm$event, z = dataKm$trt))
.df <- .df[do.call(order, .df[, c("z", "x"), drop = FALSE]), , drop = FALSE]
.fit <- survival::survfit(
survival::Surv(time = x, event = y, type = "right") ~ z, .df)
.fit <- data.frame(x = .fit$time, y = .fit$surv, nrisk = .fit$n.risk,
nevent = .fit$n.event, ncensor= .fit$n.censor, upper = .fit$upper,
lower = .fit$lower)
.df <- .df[!duplicated(.df[,c("x", "z")]), ]
.df <- .fit <- data.frame(.fit, .df[, c("z"), drop = FALSE])
.df <- .fit <- rbind(unique(data.frame(x = 0, y = 1, nrisk = NA, nevent = NA,
ncensor = NA, upper = 1, lower = 1, .df[, c("z"), drop = FALSE])), .fit)
.cens <- subset(.fit, ncensor == 1)
ggplot(data = .fit, aes(x = x, y = y, colour = z)) +
RcmdrPlugin.KMggplot2::geom_stepribbon(data = .fit,
aes(x = x, ymin = lower, ymax = upper, fill = z), alpha = 0.25,
colour = "transparent", show.legend = FALSE, kmplot = TRUE) +
geom_step(size = 1.5) +
geom_linerange(data = .cens, aes(x = x, ymin = y, ymax = y + 0.02),
size = 1.5) +
scale_x_continuous(breaks = seq(0, 21, by = 7), limits = c(0, 21)) +
scale_y_continuous(limits = c(0, 1), expand = c(0.01, 0)) +
scale_colour_brewer(palette = "Set1") +
scale_fill_brewer(palette = "Set1") +
xlab("Time from entry") +
ylab("Proportion of survival") +
labs(colour = "trt") +
theme_bw(base_size = 14, base_family = "sans") +
theme(legend.position = "right")
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