plot.tvcure: Plot visual information related to a tvcure object.

In tvcure: Additive Cure Survival Model with Time-Varying Covariates

Plot visual information related to a tvcure object.

Description

Visualization of the estimated additive terms and of the reference (cumulative) hazard function in a tvcure object.

Usage

## S3 method for class 'tvcure'
plot(x, ngrid=300, ci.level=.95, pages=0, select=NULL,
                             fill=TRUE, pointwise=TRUE, mar=c(4,5,1,1),
                             xlim0=NULL, ylim0=NULL,
                             xlim1=NULL, ylim1=NULL, xlim2=NULL, ylim2=NULL,
                             equal.ylims=TRUE,...)

Arguments

x	a tvcure.object.
ngrid	(optional) number of points used to plot the fitted additive terms. (Default: 300).
ci.level	(optional) nominal level for the plotted pointwise credible intervals. (Default: 0.95).
pages	The number of pages over which to spread the output. For example, if pages=1 then all terms will be plotted on one page with the layout performed automatically. Set to 0 to have the routine leave all graphics settings as they are. (Default 0).
select	Allows the plot for a single model term to be selected for printing. e.g. if you just want the plot for the second smooth term set select=2. The plot of the reference hazard f_0(t) and cumulative hazard F_0(t) functions is provided when select=0. When select=-1, only the reference hazard is plotted.(Default: NULL).
fill	Logical indicating whether credible regions should be greyed out. (Default: TRUE).
pointwise	Logical indicating whether only pointwise credible intervals should be plotted for additive terms. When FALSE, simultaneous credible regions are also provided. (Default: TRUE).
mar	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot. (Default: c(4,5,1,1)).
xlim0	Vector of length 2 specifying x-axis limits when plotting the estimated reference hazard function \exp(\beta_0)f_0(t).
ylim0	Vector of length 2 specifying y-axis limits when plotting the estimated reference hazard function \exp(\beta_0)f_0(t).
xlim1	Vector of length 2 specifying (common) x-axis limits when plotting the fitted additive term(s) in the long-term survival submodel. (Default: NULL).
ylim1	Vector of length 2 specifying (common) y-axis limits when plotting the fitted additive term(s) in the long-term survival submodel. (Default: NULL).
xlim2	Vector of length 2 specifying (common) x-axis limits when plotting the fitted additive term(s) in the short-term survival submodel. (Default: NULL).
ylim2	Vector of length 2 specifying (common) y-axis limits when plotting the fitted additive term(s) in the short-term survival submodel. (Default: NULL).
equal.ylims	logical indicating if the same y-limits must be used when plotting the fitted additive terms from the same submodel. It can be overriden by non-NULL values for ylim1 or ylim2. (Default: TRUE).
...	additional generic plotting arguments.

Details

Plot of the fitted additive terms, as well as of the reference hazard f_0(t) and cumulative hazard F_0(t) functions of the fitted tvcure model in x.

Value

In addition to the plots, an invisible list generated by the additive.tvcure function is returned.

Author(s)

Philippe Lambert [e-mail] based on the plot.gam function in mgcv for the pages argument.

References

Lambert, P. and Kreyenfeld, M. (2025). Time-varying exogenous covariates with frequently changing values in double additive cure survival model: an application to fertility. Journal of the Royal Statistical Society, Series A. <doi:10.1093/jrsssa/qnaf035>

See Also

tvcure, tvcure.object, print.tvcure

Examples

require(tvcure)
## Simulated data generation
beta = c(beta0=.4, beta1=-.2, beta2=.15) ; gam = c(gam1=.2, gam2=.2)
data = simulateTVcureData(n=500, seed=123, beta=beta, gam=gam,
                          RC.dist="exponential",mu.cens=550)$rawdata
## TVcure model fitting
tau.0 = 2.7 ; lambda1.0 = c(40,15) ; lambda2.0 = c(25,70) ## Optional
model = tvcure(~z1+z2+s(x1)+s(x2), ~z3+z4+s(x3)+s(x4), data=data,
               tau.0=tau.0, lambda1.0=lambda1.0, lambda2.0=lambda2.0)
plot(model,pages=1)

tvcure documentation built on April 12, 2025, 1:58 a.m.