The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

geom_stepribbon

Triad sou.

2015-12-31

The geom_stepribbon is an extension of the geom_ribbon, and is optimized for Kaplan-Meier plots with pointwise confidence intervals or a confidence band.

Usage

geom_stepribbon(mapping = NULL, data = NULL, stat = "identity",
  position = "identity", na.rm = FALSE, show.legend = NA,
  inherit.aes = TRUE, kmplot = FALSE, ...)

The additional argument

Other arguments are the same as the geom_ribbon.

Example

require("ggplot2")
## Loading required package: 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))
## Warning in RcmdrPlugin.KMggplot2::geom_stepribbon(aes(ymin = level - 1, :
## Ignoring unknown parameters: `orientation` and `outline.type`

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")
## Warning in RcmdrPlugin.KMggplot2::geom_stepribbon(data = .fit, aes(x = x, :
## Ignoring unknown parameters: `orientation` and `outline.type`
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.