plot.summary.sievePH: Plotting Mark-Specific Proportional Hazards Model Fits

Description

plot method for class summary.sievePH. For univariate marks, it plots point and interval estimates of the mark-specific treatment effect parameter specified by contrast in summary.sievePH, and, optionally, scatter/box plots of the observed mark values by treatment. For bivariate marks, plotting is restricted to the point estimate, which is displayed as a surface. No plotting is provided for marks of higher dimensions.

Usage

# S3 method for summary.sievePH
plot(
  x,
  mark = NULL,
  tx = NULL,
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  xtickAt = NULL,
  xtickLab = NULL,
  ytickAt = NULL,
  ytickLab = NULL,
  xlab = NULL,
  ylab = NULL,
  zlab = NULL,
  txLab = c("Placebo", "Treatment"),
  title = NULL,
  ...
)

Value

None. The function is called solely for plot generation.

Arguments

x: an object returned by summary.sievePH
mark: either a numeric vector specifying a univariate continuous mark or a data frame specifying a multivariate continuous mark. For subjects with a right-censored time-to-event, the value(s) in mark should be set to NA.
tx: a numeric vector indicating the treatment group (1 if treatment, 0 if placebo)
xlim: a numeric vector of length 2 specifying the x-axis range (NULL by default)
ylim: a numeric vector of length 2 specifying the y-axis range (NULL by default)
zlim: a numeric vector of length 2 specifying the z-axis range in a 3-dimensional plot (NULL by default)
xtickAt: a numeric vector specifing the position of x-axis tickmarks (NULL by default)
xtickLab: a numeric vector specifying labels for tickmarks listed in xtickAt. If NULL (default), the labels are determined by xtickAt.
ytickAt: a numeric vector specifing the position of y-axis tickmarks (NULL by default)
ytickLab: a numeric vector specifying labels for tickmarks listed in ytickAt. If NULL (default), the labels are determined by ytickAt.
xlab: a character string specifying the x-axis label (NULL by default)
ylab: a character string specifying the y-axis label (NULL by default)
zlab: a character string specifying the z-axis label in a 3-dimensional plot (NULL by default)
txLab: a character vector of length 2 specifying the placebo and treatment labels (in this order). The default labels are placebo and treatment.
title: a character string specifying the plot title (NULL by default)
...: other arguments to be passed to plotting functions

Details

For bivariate marks, markGrid in summary.sievePH must have equally spaced values for each component.

Examples

Run this code

n <- 500
tx <- rep(0:1, each=n/2)
tm <- c(rexp(n/2, 0.2), rexp(n/2, 0.2 * exp(-0.4)))
cens <- runif(n, 0, 15)
eventTime <- pmin(tm, cens, 3)
eventInd <- as.numeric(tm <= pmin(cens, 3))
mark <- ifelse(eventInd==1, c(rbeta(n/2, 2, 5), rbeta(n/2, 2, 2)), NA)
markRng <- range(mark, na.rm=TRUE)

# fit a model with a univariate mark
fit <- sievePH(eventTime, eventInd, mark, tx)
sfit <- summary(fit, markGrid=seq(markRng[1], markRng[2], length.out=10))
plot(sfit, mark, tx)