plot Information-Theoretic: Provides plots of trial- and individual-level surrogacy in the Information-Theoretic framework

Description

Produces plots that provide a graphical representation of trial- and/or individual-level surrogacy (R2_ht and R2_h) based on the Information-Theoretic approach of Alonso & Molenberghs (2007).

Usage

# S3 method for FixedContContIT
plot(x, Trial.Level=TRUE, Weighted=TRUE, Indiv.Level=TRUE,
Xlab.Indiv, Ylab.Indiv, Xlab.Trial, Ylab.Trial, Main.Trial, Main.Indiv,
Par=par(oma=c(0, 0, 0, 0), mar=c(5.1, 4.1, 4.1, 2.1)), ...)
# S3 method for MixedContContIT
plot(x, Trial.Level=TRUE, Weighted=TRUE, Indiv.Level=TRUE,
Xlab.Indiv, Ylab.Indiv, Xlab.Trial, Ylab.Trial, Main.Trial, Main.Indiv,
Par=par(oma=c(0, 0, 0, 0), mar=c(5.1, 4.1, 4.1, 2.1)), ...)

Arguments

x: An object of class MixedContContIT or FixedContContIT.
Trial.Level: Logical. If Trial.Level=TRUE, a plot of the trial-specific treatment effects on the true endpoint against the trial-specific treatment effect on the surrogate endpoints is provided (as a graphical representation of \(R_{ht}\)). Default TRUE.
Weighted: Logical. This argument only has effect when the user requests a trial-level surrogacy plot (i.e., when Trial.Level=TRUE in the function call). If Weighted=TRUE, the circles that depict the trial-specific treatment effects on the true endpoint against the surrogate endpoint are proportional to the number of patients in the trial. If Weighted=FALSE, all circles have the same size. Default TRUE.
Indiv.Level: Logical. If Indiv.Level=TRUE, a plot of the trial- and treatment-corrected residuals of the true and surrogate endpoints is provided. This plot provides a graphical representation of \(R_{h}\). Default TRUE.
Xlab.Indiv: The legend of the X-axis of the plot that depicts individual-level surrogacy. Default "Residuals for the surrogate endpoint (\(\varepsilon_{Sij}\))".
Ylab.Indiv: The legend of the Y-axis of the plot that depicts individual-level surrogacy. Default "Residuals for the true endpoint (\(\varepsilon_{Tij}\))".
Xlab.Trial: The legend of the X-axis of the plot that depicts trial-level surrogacy. Default "Treatment effect on the surrogate endpoint (\(\alpha_{i}\))".
Ylab.Trial: The legend of the Y-axis of the plot that depicts trial-level surrogacy. Default "Treatment effect on the true endpoint (\(\beta_{i}\))".
Main.Indiv: The title of the plot that depicts individual-level surrogacy. Default "Individual-level surrogacy".
Main.Trial: The title of the plot that depicts trial-level surrogacy. Default "Trial-level surrogacy".
Par: Graphical parameters for the plot. Default par(oma=c(0, 0, 0, 0), mar=c(5.1, 4.1, 4.1, 2.1)).
...: Extra graphical parameters to be passed to plot().

Author

Wim Van der Elst, Ariel Alonso, & Geert Molenberghs

References

Alonso, A, & Molenberghs, G. (2007). Surrogate marker evaluation from an information theory perspective. Biometrics, 63, 180-186.

Examples

Run this code

if (FALSE) {
## Load ARMD dataset
data(ARMD)

## Conduct a surrogacy analysis, using a weighted reduced univariate fixed effect model:
Sur <- MixedContContIT(Dataset=ARMD, Surr=Diff24, True=Diff52, Treat=Treat, Trial.ID=Center,
Pat.ID=Id, Model=c("Full"))

## Request both trial- and individual-level surrogacy plots. In the trial-level plot,
## make the size of the circles proportional to the number of patients in a trial:
plot(Sur, Trial.Level=TRUE, Weighted=TRUE, Indiv.Level=TRUE)

## Make a trial-level surrogacy plot using filled blue circles that
## are transparent (to make sure that the results of overlapping trials remain
## visible), and modify the title and the axes labels of the plot:
plot(Sur, pch=16, col=rgb(.3, .2, 1, 0.3), Indiv.Level=FALSE, Trial.Level=TRUE,
Weighted=TRUE, Main.Trial=c("Trial-level surrogacy (ARMD dataset)"),
Xlab.Trial=c("Difference in vision after 6 months (Surrogate)"),
Ylab.Trial=c("Difference in vision after 12 months (True enpoint)"))

## Add the estimated R2_ht value in the previous plot at position (X=-2.2, Y=0)
## (the previous plot should not have been closed):
R2ht <- format(round(as.numeric(Sur$R2ht[1]), 3))
text(x=-2.2, y=0, cex=1.4, labels=(bquote(paste("R"[ht]^{2}, "="~.(R2ht)))))

## Make an Individual-level surrogacy plot with red squares to depict individuals
## (rather than black circles):
plot(Sur, pch=15, col="red", Indiv.Level=TRUE, Trial.Level=FALSE)
}