| tbox {Epi} | R Documentation |
Boxes can be drawn with text (tbox) or a cross (dbox), and
arrows pointing between the boxes (boxarr) can be drawn
automatically not overlapping the boxes. Lexis objects
can be used to generate displays with person-years and events.
tbox( txt, x, y, w, h,
font = 2, txt.col = "black", lwd = 2,
border = "black", col = "transparent", ...)
dbox( x, y, w, h=w,
font=2, cross.col="black", cwd=5,
lwd=2, border="black", col="transparent" )
boxarr( b1, b2, offset=FALSE, ... )
boxes( obj, ... )
## S3 method for class 'Lexis':
boxes( obj, file,
wmult = 1.5,
hmult = 1.5*wmult,
cex = 1.5,
show = inherits( obj, "Lexis" ),
show.Y = show,
show.D = show,
scale.Y = 1,
digits.Y = 1,
eq.wd = TRUE,
eq.ht = TRUE, ... )
fillarr( x1, y1, x2, y2, fr=0.8,
angle=17, lwd=2, length=par("pin")[1]/30, ... )
txt |
Text to be placed inside the box. |
x |
x-coordinate of center of box. |
y |
y-coordinate of center of box. |
w |
width of box. |
h |
height of box. |
font |
Font for the text. |
txt.col |
Color for the text. |
lwd |
Line width of the box / arrow. |
border |
Color of the box border. |
col |
Background color for the interior of the box. |
... |
Arguments to be passed on to the call of other functions. |
cross.col |
Color of the cross. |
cwd |
Width of the lines in the cross. |
b1 |
Coordinates of the "from" box. A vector with 4 components,
x, y, w, h. |
b2 |
Coordinates of the "to" box. |
offset |
Logical. Should the arrow be offset a bit to the left. |
obj |
A Lexis object, or a transition matrix; that
is a matrix |
file |
Name of the file with the code reproducing the plot. |
wmult |
Multiplier for the width of the box relative to the width of the text in the box. |
hmult |
Multiplier for the height of the box relative to the height of the text in the box. |
cex |
Character expansion for text in the box. |
show |
Should person-years and transitions be put in the plot.
Ignored if obj is not a Lexis object. |
show.Y |
Should person-years be put in the boxes.
Ignored if obj is not a Lexis object. |
show.D |
Should transitions be put alongside the arrows.
Ignored if obj is not a Lexis object. |
scale.Y |
What scale should be used for annotation of person-years. |
digits.Y |
How many digtis after the decimal point should be used for the person-years. |
eq.wd |
Should boxes all have the same width? |
eq.ht |
Should boxes all have the same height? |
x1 |
x-coordinate of the starting point. |
y1 |
y-coordinate of the starting point. |
x2 |
x-coordinate of the ending point. |
y2 |
y-coordinate of the ending point. |
fr |
Length of the arrow as the fraction of the distance between the boxes. |
angle |
What angle should the arrow-head have? |
length |
Length of the arrow head in inches. |
These functions are designed to facilitate the drawing of multistate models, mainly by automatic calculation of the arrows between boxes.
tbox draws a box with centered text, and returns a vector of
location, height and width of the box. This is used when drawing
arrows between boxes. dbox draws a box with a cross,
symbolizing a death state. boxarr draws an arrow between two
boxes, making sure it does not intersect the boxes. Only straight
lines are drawn.
boxes.Lexis takes as input a Lexis object sets up an empty plot
area (with axes 0 to 100 in both directions) and prompts you to click
on the locations for the state boxes, and then draws arrows implied by
the actual transitions in the Lexis object.
A transition matrix can also be supplied, in which case the row/column names are used as state names.
Optionally returns the R-code reproducing the plot in a file, which can be useful if you want to produce exactly the same plot with differing arrow colors etc.
boxarr draws an arrow between two boxes, on the line conneting
the two box centers. The offset argument is used to offset the
arrow a bit to the left (in the direction) on order to accomodate
arrows both waus between boxes. boxarr returns a named list
wit´h elements x, y and d, wher the two formewr
is the location of the midpoint and the latter is a unit vector in the
direction of the arrow, which is used by boxes.Lexis to
position the annotation of arrows with the number of transitions.
fill.arr is just a utility drawing nicer arrows than the default
arrows command, basically by using filled arrow-heads; called
by boxarr.
The functions tbox and dbox return the location and
dimension of the boxes, c(x,y,w,h), which are designed to be used
as input to the boxarr function.
The boxarr function returns the coordinates (as a named
list with names x and y) of the midpoint of the
arrow, designated to be used for annotation of the arrow.
Bendix Carstensen
par( mar=c(0,0,0,0), cex=1.5 )
plot( NA,
bty="n",
xlim=0:1*100, ylim=0:1*100, xaxt="n", yaxt="n", xlab="", ylab="" )
bw <- tbox( "Well" , 10, 60, 22, 10, txt.col="blue" )
bo <- tbox( "other Ca", 45, 80, 22, 10, txt.col="gray" )
bc <- tbox( "Ca" , 45, 60, 22, 10, txt.col="red" )
bd <- tbox( "DM" , 45, 40, 22, 10, txt.col="blue" )
bcd <- tbox( "Ca + DM" , 80, 60, 22, 10, txt.col="gray" )
bdc <- tbox( "DM + Ca" , 80, 40, 22, 10, txt.col="red" )
boxarr( bw, bo , col=gray(0.7), lwd=3 )
# Note the argument adj= can takes values outside (0,1)
text( boxarr( bw, bc , col="blue", lwd=3 ),
expression( lambda[Well] ), col="blue", adj=c(1,-0.2), cex=0.8 )
boxarr( bw, bd , col=gray(0.7) , lwd=3 )
boxarr( bc, bcd, col=gray(0.7) , lwd=3 )
text( boxarr( bd, bdc, col="blue", lwd=3 ),
expression( lambda[DM] ), col="blue", adj=c(1.1,-0.2), cex=0.8 )
# Set up a transition matrix allowing recovery
tm <- rbind( c(NA,1,1), c(1,NA,1), c(NA,NA,NA) )
rownames(tm) <- colnames(tm) <- c("Cancer","Recurrence","Dead")
## Not run: boxes.Lexis( tm, file="" )
# Set up a Lexis object
data(DMlate)
str(DMlate)
dml <- Lexis( entry=list(Per=dodm, Age=dodm-dobth, DMdur=0 ),
exit=list(Per=dox),
exit.status=factor(!is.na(dodth),labels=c("DM","Dead")),
data=DMlate )
# Split follow-up at Insulin
dmi <- cutLexis( dml, cut=dml$doins, new.state="Ins", pre="DM" )
summary( dmi )
## Not run: boxes( dmi, file="" )
# Set up a bogus recovery date
dmi$dorec <- dmi$doins + runif(nrow(dmi),0.5,10)
dmi$dorec[dmi$dorec>dmi$dox] <- NA
dmR <- cutLexis( dmi, cut=dmi$dorec, new.state="DM", pre="Ins" )
summary( dmR )
## Not run: boxes( dmR )