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plotEffects

Plotting time-varying effects from a risk regression model.

Description

Plot time-varying effects from a risk regression model.

Usage

plotEffects(
  x,
  formula,
  level,
  ref.line = TRUE,
  conf.int = 0.95,
  xlim,
  ylim,
  xlab = "Time",
  ylab = "Cumulative coefficient",
  col,
  lty,
  lwd,
  add = FALSE,
  legend,
  axes = TRUE,
  ...
)

Arguments

x

Fitted object obtained with one of ARR, LRR, riskRegression.
formula

A formula to specify the variable(s) whose regression coefficients should be plotted.
level

For categorical variables the level (group) whose contrast to the reference level (group) should be plotted.
ref.line

Logical. If TRUE then add a horizontal line at zero.
conf.int

Logical. If TRUE then add confidence limits. Can be controlled using smart arguments. See examples
xlim

See plot
ylim

See plot
xlab

See plot
ylab

See plot
col

A vector of colors for the regression coefficients.
lty

A vector of line types for the regression coefficients.
lwd

A vector of line thicknesses for the regression coefficients.
add

Logical. If TRUE then add lines to an existing plot.
legend

Logical. If TRUE then add a legend. Can be controlled using smart arguments. See examples.
axes

Logical. If FALSE then do not draw axes.
...

Used for transclusion of smart arguments for plot, axis. See function SmartControl from prodlim.

Author(s)

Thomas H. Scheike ts@biostat.ku.dk

Thomas A. Gerds tag@biostat.ku.dk

Examples

library(survival)
library(prodlim)
data(Melanoma)

fit.tarr <- ARR(Hist(time,status)~strata(sex),
                data=Melanoma,
                cause=1)
plotEffects(fit.tarr)

fit.tarr <- ARR(Hist(time,status)~strata(sex)+strata(invasion),
                data=Melanoma,
                cause=1,
                times=seq(800,3000,20))
plotEffects(fit.tarr,formula=~sex)
plotEffects(fit.tarr,formula=~invasion)
plotEffects(fit.tarr,
            formula=~invasion,
            level="invasionlevel.1")

## legend arguments are transcluded:
plotEffects(fit.tarr,
            formula=~invasion,
            legend.bty="b",
            legend.cex=1)

## and other smart arguments too:
plotEffects(fit.tarr,
	    formula=~invasion,
	    legend.bty="b",
axis2.las=2,
	    legend.cex=1)
riskRegression

Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

v2020.12.08
GPL (>= 2)
Authors
Thomas Alexander Gerds [aut, cre], Paul Blanche [ctb], Rikke Mortensen [ctb], Marvin Wright [ctb], Nikolaj Tollenaar [ctb], John Muschelli [ctb], Ulla Brasch Mogensen [ctb], Brice Ozenne [aut] (<https://orcid.org/0000-0001-9694-2956>)
Initial release

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