plot.jointSurroPenalloocv: Plot of trials leave-one-out crossvalidation Outputs from the...

In frailtypack: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints

Plot of trials leave-one-out crossvalidation Outputs from the one-step Joint surrogate model for evaluating a canditate surrogate endpoint.

Description

Plot of trials leave-one-out crossvalidation Outputs for evaluating the joint surrogate model

Usage

## S3 method for class 'jointSurroPenalloocv'
plot(x, unusedtrial = NULL, xleg = "bottomleft", 
yleg = NULL, main = NULL, xlab = "Trials", 
ylab = "Log Hazard ratio of the true endpoint", 
legend = c("Beta observed", "Beta predict"), ...)

Arguments

x	An object inherent from the jointSurroPenalloocv Class
unusedtrial	Vector of unconsidered trials, may be due to the fact that the predicted treatment effects on true endpoint have an outlier. In this case, one can drop from the data the trials with very hight absolute predicted value
xleg	X-coordinate for the location of the legend.
yleg	Y-coordinate for the location of the legend, the default is NULL
main	An overall title for the plot: see title.
xlab	A title for the x axis: see title.
ylab	A title for the y axis: see title.
legend	A vector of characters string of length >= 1 to appear in the legend
...	other unused arguments.

Value

This function displays the boxplots corresponding to the number of trials in the dataset. Each boxplot includes 3 elements corresponding to the predicted treatment effect on true endpoint with the prediction interval. The circles inside or outside the boxplot represent the observed treatment effects on true endpoint. For each trial with convergence issues or outliers, the boxplot is replaced by a dash. In this case, we display in the title of the figure a vector of these trials, if argument main is set to NULL. The function returns the list of unused trials.

Author(s)

Casimir Ledoux Sofeu [e-mail], [e-mail] and Virginie Rondeau [e-mail]

References

Burzykowski T, Buyse M (2006). "Surrogate threshold effect: an alternative measure for meta-analytic surrogate endpoint validation." Pharmaceutical Statistics, 5(3), 173-186.ISSN 1539-1612.

See Also

loocv

Examples

# Generation of data to use 
 data.sim <- jointSurrSimul(n.obs=300, n.trial = 10,cens.adm=549.24,
             alpha = 1.5, theta = 3.5, gamma = 2.5, zeta = 1, sigma.s = 0.7,
             sigma.t = 0.7, cor = 0.8, betas = -1.25, betat = -1.25,
             full.data = 0, random.generator = 1, seed = 0,
             nb.reject.data = 0)

###--- Joint surrogate model ---###
 
joint.surro.sim.MCGH <- jointSurroPenal(data = data.sim, int.method = 2,
                        nb.mc = 300, nb.gh = 20, print.iter = T)
        
# Example of loocv taking into accountn ony trial 2 trials (1 and 3)
dloocv <- loocv(joint.surro.sim.MCGH, unusedtrial = c(2,4:10))

plot(x = dloocv, xleg = "topright", bty = "n")

frailtypack documentation built on Nov. 25, 2023, 9:06 a.m.