plot_rmst_curve {adjustedCurves}R Documentation

Plot Adjusted Restricted Mean Survival Time Curves

Description

A function to graphically display the Restricted Mean Survival Time (RMST) over time, using confounder-adjusted survival curves which where previously estimated using the adjustedsurv function. As the other plot functions in this package, it internally uses the ggplot2 package and allows a variety of options.

Usage

plot_rmst_curve(adjsurv, times=NULL, conf_int=FALSE,
                conf_level=0.95, interpolation="steps",
                max_t=Inf, color=TRUE, linetype=FALSE,
                facet=FALSE, size=1, alpha=1, xlab="Time",
                ylab="RMST", title=NULL, subtitle=NULL,
                legend.title="Group", legend.position="right",
                gg_theme=ggplot2::theme_classic(),
                custom_colors=NULL, custom_linetypes=NULL,
                conf_int_alpha=0.4, ...)

Arguments

adjsurv

An adjustedsurv object created using the adjustedsurv function.

times

A vector of points in time, passed to the to argument of the adjusted_rmst function or NULL (default). If NULL, the adjusted RMST is estimated at all points at which an event occurred. Otherwise it is estimated at times.

conf_int

A logical variable indicating whether the bootstrap confidence intervals should be drawn.

interpolation

Corresponds to the argument of the same name in the adjusted_rmst function.

conf_level

Corresponds to the argument of the same name in the adjusted_rmst function.

max_t

A number indicating the latest survival time which is to be plotted.

color

A logical variable indicating whether the curves should be colored differently. The custom_colors argument can be used to directly specify which colors to use. Set to FALSE to keep the plot black and white.

linetype

A logical variable indicating whether the curves should have different linetypes. The custom_linetypes argument can be used to directly specify which linetypes to use. Set to FALSE to keep all lines solid.

facet

A logical variable indicating whether the curves should be in different facets.

size

A number controlling the thickness of the RMST curves.

alpha

A number controlling the transparency level of the RMST curves.

xlab

A character string to be used as the X-Axis label of the plot.

ylab

A character string to be used as the Y-Axis label of the plot.

title

A character string to be used as the title of the plot. Set to NULL if no title should be used.

subtitle

A character string to be used as the subtitle of the plot. Set to NULL if no subtitle should be used.

legend.title

A character string to be used as the title of the legend. Set to NULL if no legend should be included.

legend.position

A character string specifying the position of the legend. Ignored if legend_title=NULL.

gg_theme

A ggplot2 theme object which will be used for the plot.

custom_colors

A (named) vector to specify the colors of each adjusted RMST curve and possibly its confidence region. Set to NULL to use the ggplot2 default values. Ignored if color=FALSE.

custom_linetypes

A (named) vector to specify the linetype of each adjusted RMST curve. Set to NULL to use the ggplot2 default values. Ignored if color=FALSE. Ignored if linetype=FALSE.

conf_int_alpha

A number indicating the level of transparency that should be used when drawing the confidence regions.

...

Currently not used.

Details

This function simply calls the adjusted_rmst for a range of to values, getting adjusted RMST estimates over the whole range of the survival curves. Those estimates are then plotted as a curve with the adjusted RMST replacing the survival probability on the Y-Axis. For a brief description on the RMST and how it is calculated in this package, see the documentation of the adjusted_rmst function. Literature describing the RMST Curve Plots in more detail is given in the references section.

The RMST curve can only be created for adjusted survival curves. A similar graphic for the adjusted CIFs can be created by utilizing the adjusted Restricted Mean Time Lost (RMTL). The calculation of that statistic is implemented in the adjusted_rmtl function and the associated curve can be created using the plot_rmtl_curve function.

If confidence intervals are specified and there are many points in time in times, this function might get very slow. It will be even slower if multiple imputation was also used when creating the adjustedsurv object.

Value

Returns a ggplot2 object.

Author(s)

Robin Denz

References

Lihui Zhao, Brian Claggett, Lu Tian, Hajime Uno, Marc A. Pfeffer, Scott D. Solomon, Lorenzo Trippa, and L. J. Wei (2016). "On the Restricted Mean Survival Time Curve in Survival Analysis". In: Biometrics 72.1, pp. 215-221

Jason J. Z. Liao, Frank Liu, and Wen-Chi Wu (2020). "Dynamic RMST Curves for Survival Analysis in Clinical Trials". In: BMC Medical Research Methodology 20.218

See Also

adjustedsurv, adjusted_rmst, ggplot

Examples

library(adjustedCurves)
library(survival)
library(ggplot2)

set.seed(42)

# simulate some data as example
sim_dat <- sim_confounded_surv(n=50, max_t=1.2)
sim_dat$group <- as.factor(sim_dat$group)

# estimate a cox-regression for the outcome
cox_mod <- coxph(Surv(time, event) ~ x1 + x2 + x3 + x4 + x5 + x6 + group,
                 data=sim_dat, x=TRUE)


# use it to calculate adjusted survival curves with bootstrapping
adjsurv <- adjustedsurv(data=sim_dat,
                        variable="group",
                        ev_time="time",
                        event="event",
                        method="direct",
                        outcome_model=cox_mod,
                        conf_int=TRUE,
                        bootstrap=TRUE,
                        n_boot=15) # should be much bigger in reality

# plot the curves with default values
plot_rmst_curve(adjsurv)

# plot with confidence intervals
plot_rmst_curve(adjsurv, conf_int=TRUE)

# plot with some custom options
plot_rmst_curve(adjsurv, max_t=0.5, linetype=TRUE,
                custom_colors=c("green", "blue"))

[Package adjustedCurves version 0.11.0 Index]