plot.Hist: Box-arrow diagrams for multi-state models.

In prodlim: Product-Limit Estimation for Censored Event History Analysis

Box-arrow diagrams for multi-state models.

Description

Automated plotting of the states and transitions that characterize a multi states model.

Usage

## S3 method for class 'Hist'
plot(
  x,
  nrow,
  ncol,
  box.width,
  box.height,
  box.padding,
  xbox.position,
  ybox.position,
  stateLabels,
  arrowLabels,
  arrowLabelStyle = "symbolic",
  arrowLabelSymbol = "lambda",
  changeArrowLabelSide,
  curved,
  tagBoxes = FALSE,
  startCountZero = TRUE,
  oneFitsAll,
  margin,
  cex,
  rasta = FALSE,
  verbose = FALSE,
  ...
)

Arguments

x	An object of class Hist.
nrow	the number of graphic rows
ncol	the number of graphic columns
box.width	the widths of the boxes on the scale from 0 to 100
box.height	the heights of the boxes on the scale from 0 to 100
box.padding	how much room there should be between the label and the border of a box. Two values on the scale from 0 to 100: the first for the horizontal x-direction and the second for the vertical y-direction padding.
xbox.position	the x box positions (left lower corner) on the scale from 0 to 100.
ybox.position	the y box positions (left lower corner) on the scale from 0 to 100.
stateLabels	Vector of names to appear in the boxes (states). Defaults to attr(x,"state.names"). The boxes can also be individually labeled by smart arguments of the form box3.label="diseased", see examples.
arrowLabels	Vector of labels to appear in the boxes (states). One for each arrow. The arrows can also be individually labeled by smart arguments of the form arrow1.label=paste(expression(eta(s,u))), see examples.
arrowLabelStyle	Either "symbolic" for automated symbolic arrow labels, or "count" for arrow labels that reflect the number of transitions in the data.
arrowLabelSymbol	Symbol for automated symbolic arrow labels. Defaults to "lambda".
changeArrowLabelSide	A vector of mode logical (TRUE,FALSE) one for each arrow to change the side of the arrow on which the label is placed.
curved	The curvature of curved arrows via diagram::curvedarrow. Experimental. Values between 0 (no curvature) and 1 are meaningful.
tagBoxes	Logical. If TRUE the boxes are numbered in the upper left corner. The size can be controlled with smart argument boxtags.cex. The default is boxtags.cex=1.28.
startCountZero	Control states numbers for symbolic arrow labels and box tags.
oneFitsAll	If FALSE then boxes have individual size, depending on the size of the label, otherwise all boxes have the same size dependent on the largest label.
margin	Set the figure margin via par(mar=margin). Less than 4 values are repeated.
cex	Initial cex value for the state and the arrow labels.
rasta	For construction purposes.
verbose	If TRUE echo various things.
...	Smart control of arguments for the subroutines text (box label), rect (box), arrows, text (arrow label). Thus the three dots can be used to draw individual boxes with individual labels, arrows and arrow labels. E.g. arrow2.label="any label" changes the label of the second arrow. See examples.

Note

Use the functionality of the unix program ‘dot’ http://www.graphviz.org/About.php via R package Rgraphviz to obtain more complex graphs.

Author(s)

Thomas A Gerds [e-mail]

See Also

HistSmartControl

Examples

## A simple survival model

SurvFrame <- data.frame(time=1:10,status=c(0,1,1,0,0,1,0,0,1,0))
SurvHist <- with(SurvFrame,Hist(time,status))
plot(SurvHist)
plot(SurvHist,box2.col=2,box2.label="experienced\nR user")
plot(SurvHist,
     box2.col=2,
     box1.label="newby",
     box2.label="experienced\nR user",
     oneFitsAll=FALSE,
     arrow1.length=.5,
     arrow1.label="",
     arrow1.lwd=4)

## change the cex of all box labels:
plot(SurvHist,
     box2.col=2,
     box1.label="newby",
     box2.label="experienced\nR user",
     oneFitsAll=FALSE,
     arrow1.length=.5,
     arrow1.label="",
     arrow1.lwd=4,
     label.cex=1)

## change the cex of single box labels:
plot(SurvHist,
     box2.col=2,
     box1.label="newby",
     box2.label="experienced\nR user",
     oneFitsAll=FALSE,
     arrow1.length=.5,
     arrow1.label="",
     arrow1.lwd=4,
     label1.cex=1,
     label2.cex=2)


## The pbc data set from the survival package
library(survival)
data(pbc)
plot(with(pbc,Hist(time,status)),
     stateLabels=c("randomized","transplant","dead"),
     arrowLabelStyle="count")

## two competing risks
comprisk.model <- data.frame(time=1:3,status=1:3)
CRHist <- with(comprisk.model,Hist(time,status,cens.code=2))
plot(CRHist)
plot(CRHist,arrow1.label=paste(expression(eta(s,u))))

plot(CRHist,box2.label="This\nis\nstate 2",arrow1.label=paste(expression(gamma[1](t))))
plot(CRHist,box3.label="Any\nLabel",arrow2.label="any\nlabel")

## change the layout
plot(CRHist,
     box1.label="Alive",
     box2.label="Dead\n cause 1",
     box3.label="Dead\n cause 2",
     arrow1.label=paste(expression(gamma[1](t))),
     arrow2.label=paste(expression(eta[2](t))),
     box1.col=2,
     box2.col=3,
     box3.col=4,
     nrow=2,
     ncol=3,
     box1.row=1,
     box1.column=2,
     box2.row=2,
     box2.column=1,
     box3.row=2,
     box3.column=3)

## more competing risks
comprisk.model2 <- data.frame(time=1:4,status=1:4)
CRHist2 <- with(comprisk.model2,Hist(time,status,cens.code=2))
plot(CRHist2,box1.row=2)

## illness-death models
illness.death.frame <- data.frame(time=1:4,
				  from=c("Disease\nfree",
                                      "Disease\nfree",
                                      "Diseased",
                                      "Disease\nfree"),
				  to=c("0","Diseased","Dead","Dead"))
IDHist <- with(illness.death.frame,Hist(time,event=list(from,to)))
plot(IDHist)

## illness-death with recovery
illness.death.frame2 <- data.frame(time=1:5,
from=c("Disease\nfree","Disease\nfree","Diseased","Diseased","Disease\nfree"),
to=c("0","Diseased","Disease\nfree","Dead","Dead"))
IDHist2 <- with(illness.death.frame2,Hist(time,event=list(from,to)))
plot(IDHist2)

## 4 state models
x=data.frame(from=c(1,2,1,3,4),to=c(2,1,3,4,1),time=1:5)
y=with(x,Hist(time=time,event=list(from=from,to=to)))
plot(y)

## moving the label of some arrows

d <- data.frame(time=1:5,from=c(1,1,1,2,2),to=c(2,3,4,3,4))
h <- with(d,Hist(time,event=list(from,to)))
plot(h,box.padding=c(5,2),
tagBoxes=TRUE,
stateLabels=c("Remission\nwithout\nGvHD",
    "Remission\nwith\nGvHD",
    "Relapse",
    "Death\nwithout\nrelapse"),
arrowLabelSymbol='alpha',
arrowlabel3.x=35,
arrowlabel3.y=53,
arrowlabel4.y=54,
arrowlabel4.x=68)

##'

prodlim documentation built on June 24, 2024, 5:08 p.m.