riskRegression (version 2019.11.03)

plotRisk: plot predicted risks

Description

plot predicted risks

Usage

plotRisk(x, models, times, xlim = c(0, 1), ylim = c(0, 1), xlab, ylab,
  col, pch = 3, cex = 1, preclipse = 0, preclipse.shade = FALSE,
  ...)

Arguments

x

Object obtained with function Score

models

Choice of two models to plot. The predicted risks of the first (second) are shown along the x-axis (y-axis).

times

Time point specifying the prediction horizon.

xlim

x-axis limits

ylim

y-axis limits

xlab

x-axis labels

ylab

y-axis labels

col

colour

pch

point type

cex

point size

preclipse

Value between 0 and 1 defining the preclipse area

preclipse.shade

Logical. If TRUE shade the area of clinically meaningful change.

...

Used to control the subroutines: plot, axis, lines, barplot, legend. See SmartControl.

Value

a nice graph

Details

Two rival prediction models are applied to the same data.

Examples

# NOT RUN {
library(prodlim)
## uncensored
learndat = sampleData(40,outcome="binary")
testdat = sampleData(40,outcome="binary")
lr1 = glm(Y~X1+X2+X7+X9,data=learndat,family="binomial")
lr2 = glm(Y~X3+X5+X6,data=learndat,family="binomial")
xb=Score(list("LR(X1+X2+X7+X9)"=lr1,"LR(X3+X5+X6)"=lr2),formula=Y~1,
         data=testdat,summary="risks",null.model=0L)
plotRisk(xb)
## survival
library(survival)
learndat = sampleData(40,outcome="survival")
testdat = sampleData(40,outcome="survival")
cox1 = coxph(Surv(time,event)~X1+X2+X7+X9,data=learndat,x=TRUE)
cox2 = coxph(Surv(time,event)~X3+X5+X6,data=learndat,x=TRUE)
xs=Score(list("Cox(X1+X2+X7+X9)"=cox1,"Cox(X3+X5+X6)"=cox2),formula=Surv(time,event)~1,
         data=testdat,summary="risks",null.model=0L,times=c(3,5,6))
plotRisk(xs,times=5)
## competing risk
# }
# NOT RUN {
library(prodlim)
library(survival)
set.seed(8)
learndat = sampleData(80,outcome="competing.risk")
testdat = sampleData(140,outcome="competing.risk")
m1 = FGR(Hist(time,event)~X2+X7+X9,data=learndat,cause=1)
m2 = CSC(Hist(time,event)~X2+X7+X9,data=learndat,cause=1)
xcr=Score(list("FGR"=m1,"CSC"=m2),formula=Hist(time,event)~1,
         data=testdat,summary="risks",null.model=0L,times=c(3,5))
plotRisk(xcr,times=1)
# }