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Plot estimated treatment effects

Source: R/plot_ate.R
plot_ate.Rd

This function plots the estimated treatment effect, defined as the difference in potential cumulative incidences under treated and control groups, along with pointwise confidence intervals.

Usage

plot_ate(
  fit,
  decrease = FALSE,
  conf.int = 0.95,
  xlab = "Time",
  ylim = c(-1, 1),
  xlim = NULL,
  plot.configs = list(ylab = NULL, main = NULL, lty = 1, lwd = 2, col = "black",
    add.null.line = TRUE, null.line.lty = 2, ci.lty = 5, ci.lwd = 1.5, ci.col =
    "darkgrey"),
  ...
)

Arguments

fit

A fitted object returned by the function tteICE, surv.tteICE, or scr.tteICE.

decrease

A logical value indicating the type of curve difference to display. If decrease = FALSE (default), the difference in cumulative incidence functions (CIFs) is plotted. If decrease = TRUE, the difference in survival functions is plotted instead.

conf.int

Confidence level for the pointwise confidence intervals If conf.int = NULL, no confidence intervals are provided.

xlab

Label for the x-axis.

ylim

A numeric vector of length 2 specifying the limits of the y-axis. Defaults to ylim = c(-1, 1).

xlim

A numeric vector of length 2 specifying the limits of the x-axis. If xlim = NULL (default), the limits are determined automatically from the data.

plot.configs

A named list of additional plot configurations. Common entries include:

  • ylab: character, label for the y-axis (default: ylab=NULL, use the default label).

  • main: character, title for the plot (default: main=NULL, use the default label).

  • lty: line type for effect curve (default: lty=1).

  • lwd: line width for effect curve (default: lwd=2).

  • col: line color for effect curve (default: col="black").

  • add.null.line: logical, whether to draw a horizontal line at 0 (default: add.null.line=TRUE, add the null line).

  • null.line.lty: line type for horizontal line at 0 (default: null.line.lty=2.

  • ci.lty: line type for confidence interval curves (default: ci.lty=5).

  • ci.lwd: line width for confidence interval curves (default: ci.lwd=1.5).

  • ci.col: line color for confidence interval curves (default: ci.col="darkgrey").

...

Additional graphical arguments passed to function plot.default or function curve

Value

Plot the average treatment effect (ATE) results from a tteICE object

See also

plot.default, points, curve, plot.tteICE

Examples

## Load data
data(bmt)
bmt = transform(bmt, d4=d2+d3)
A = as.numeric(bmt$group>1)
bmt$A = A

## simple model fitting and plotting
library(survival)
fit = tteICE(Surv(t2,d4,type = "mstate")~A, data=bmt)
plot_ate(fit)


## model fitting using competing risk data
fit1 = surv.tteICE(A, bmt$t2, bmt$d4, 'composite')

## Plot asymptotic confidence intervals based on explicit formulas
plot_ate(fit1, ylim=c(-0.4,0.4))


## Plot bootstrap confidence intervals
fit2 = surv.tteICE(A, bmt$t2, bmt$d4, 'natural', nboot=50) ## SE=0??
plot_ate(fit2, ylim=c(-0.4,0.4))


## Model with semicompeting risk data
fit3 = scr.tteICE(A, bmt$t1, bmt$d1, bmt$t2, bmt$d2, "composite")

## Plot asymptotic confidence intervals based on explicit formulas
plot_ate(fit3, ylim=c(-0.4,0.4),
         plot.configs=list(add.null.line=FALSE))


## Plot bootstrap confidence intervals
fit4 = scr.tteICE(A, bmt$t1, bmt$d1, bmt$t2, bmt$d2,
                  "composite", nboot=50)           ## SE=0??

plot_ate(fit4, ylim=c(-0.4,0.4),
         plot.configs=list(add.null.line=FALSE, lty=2, main=""))