prp: Plot an rpart model.
In rpart.plot: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
prp R Documentation
Plot an rpart model.
Description
Plot an rpart model.
First-time users should use rpart.plot instead,
which provides a simplified interface to this function.
For an overview, please see the package vignette
Plotting rpart trees with the rpart.plot package.
The arguments of this function are a superset of those of
rpart.plot and some of the arguments have different
defaults.
In detail the different defaults are:
| rpart.plot | prp |
type | 2 | 0 |
extra | "auto" | 0 |
fallen.leaves | TRUE | FALSE |
varlen | 0 | -8 |
faclen | 0 | 3 |
box.palette | "auto" | 0 |
The defaults are different for historical reasons: for backwards
compatibility the defaults of prp haven't changed,
whereas the defaults of rpart.plot were changed when
type="auto" and box.palette were introduced
in version 2.0.0 of this package.
Usage
prp(x=stop("no 'x' arg"),
type=0, extra=0, under=FALSE, fallen.leaves=FALSE,
nn=FALSE, ni=FALSE, yesno=TRUE,
branch=if(fallen.leaves) 1 else .2,
uniform=TRUE, left=TRUE, xflip=FALSE, yflip=FALSE,
digits=2, varlen=-8, faclen=3, roundint=TRUE,
cex=NULL, tweak=1,
clip.facs=FALSE, clip.right.labs=TRUE,
compress=TRUE, ycompress=uniform,
Margin=0, space=1, gap=NULL,
snip=FALSE, snip.fun=NULL, trace=FALSE,
box.col=0, box.palette=0,
pal.thresh=NULL, pal.node.fun=FALSE,
border.col=col,
round=NULL, leaf.round=NULL,
shadow.col=0, prefix="", suffix="", xsep=NULL,
under.percent=2, under.font=font, under.col=1, under.cex=.8,
split.cex=1, split.font=2, split.family=family, split.col=1,
split.box.col=0, split.border.col=0,
split.lty=1, split.lwd=NULL, split.round=0,
split.shadow.col=0,
split.prefix="", right.split.prefix=NULL,
split.suffix="", right.split.suffix=NULL,
facsep=",", eq=" = ", lt=" < ", ge=" >= ",
branch.col=if(is.zero(branch.type)) 1 else "gray",
branch.lty=1, branch.lwd=NULL,
branch.type=0, branch.tweak=1,
min.branch.width=.002, branch.fill=branch.col,
nn.cex=NULL, nn.font=3, nn.family="", nn.col=1,
nn.box.col=0, nn.border.col=nn.col,
nn.lty=1, nn.lwd=NULL, nn.round=.3,
yes.text="yes", no.text="no",
node.fun=NULL,
split.fun=NULL,
FUN="text",
nspace=branch, minbranch=.3, do.par=TRUE,
add.labs=TRUE, clip.left.labs=(type == 5), fam.main="",
yshift=0, yspace=space, shadow.offset=.4,
split.adj=NULL, split.yshift=0, split.space=space,
split.yspace=yspace, split.shadow.offset=shadow.offset,
nn.adj=.5, nn.yshift=0, nn.space=.8, nn.yspace=.5,
ygap=gap/2, under.ygap=.5, yesno.yshift=0,
xcompact=TRUE, ycompact=uniform, xcompact.ratio=.8, min.inter.height=4,
max.auto.cex=1, min.auto.cex=.15, ycompress.cex=.7, accept.cex=1.1,
shift.amounts=c(1.5, 2),
Fallen.yspace=.1, boxes.include.gap=FALSE,
legend.x=NULL, legend.y=NULL, legend.cex=1,
...)
Arguments
x
An rpart object. The only required argument.
type
Type of plot. Possible values:
0 Default. Draw a split label at each split
and a node label at each leaf.
1 Label all nodes, not just leaves.
Similar to text.rpart's all=TRUE.
2 Like 1 but draw the split labels below the node labels.
Similar to the plots in the CART book.
3 Draw separate split labels for the left and right directions.
4 Like 3 but label all nodes, not just leaves.
Similar to text.rpart's fancy=TRUE.
See also clip.right.labs.
5 Show the split variable name in the interior nodes.
extra
Display extra information at the nodes. Possible values:
"auto" (case insensitive)
Automatically select a value based on the model type, as follows:
extra=106 class model with a binary response
extra=104 class model with a response having more than two levels
extra=100 other models
0 Default. No extra information.
1 Display the number of observations that fall in the node
(per class for class objects;
prefixed by the number of events for poisson and exp models).
Similar to text.rpart's use.n=TRUE.
2 Class models: display the classification rate at the node,
expressed as the number of correct classifications and the number
of observations in the node.
Poisson and exp models: display the number of events.
3 Class models: misclassification rate at the node,
expressed as the number of incorrect classifications and the number
of observations in the node.
4 Class models:
probability per class of observations in the node
(conditioned on the node, sum across a node is 1).
5 Class models:
like 4 but don't display the fitted class.
6 Class models:
the probability of the second class only.
Useful for binary responses.
7 Class models:
like 6 but don't display the fitted class.
8 Class models:
the probability of the fitted class.
9 Class models:
The probability relative to all observations –
the sum of these probabilities across all leaves is 1.
This is in contrast to the options above, which give the probability
relative to observations falling in the node –
the sum of the probabilities across the node is 1.
10 Class models:
Like 9 but display the probability of the second class only.
Useful for binary responses.
11 Class models:
Like 10 but don't display the fitted class.
+100 Add 100 to any of the above to also display
the percentage of observations in the node.
For example extra=101 displays the number
and percentage of observations in the node.
Actually, it's a weighted percentage
using the weights passed to rpart.
Note: Unlike text.rpart,
by default prp uses its own routine for
generating node labels (not the function attached to the object).
See the node.fun argument.
under
Applies only if extra > 0.
Default FALSE, meaning put the extra text in the box.
Use TRUE to put the text under the box.
See also under.cex.
fallen.leaves
Default FALSE.
If TRUE, position the leaf nodes at the bottom of the graph.
nn
Display the node numbers.
Default FALSE.
(In the current implementation
some overplotting may occur with nn=TRUE.)
ni
Display the node indices,
i.e. the row numbers of the nodes in the object's frame.
Default FALSE.
yesno
One of
0 don't write yes and no on the tree
1 (default) write yes and no at the top split
2 write yes and no at all splits. Seems to work best with
fallen.leaves=TRUE, split.border.col=1.
(The yesno argument is ignored if type=3 or 4.
Use nn.col and the other nn parameters
to change the color etc. of the yes and no text.
Use yes.text and no.text to change the actual text displayed.)
branch
Controls the shape of the branch lines.
Specify a value between 0 (V shaped branches) and
1 (square shouldered branches).
Default is if(fallen.leaves) 1 else .2.
uniform
If TRUE (the default), the vertical spacing of the nodes is uniform.
If FALSE, the nodes are spaced proportionally to the fit
(more precisely, to the difference between a node's deviance and the
sum of its two children's deviances).
Very small vertical spaces are automatically artificially expanded
to make room for the labels, see minbranch.
Note: uniform=FALSE with cex=NULL (the default)
can sometimes cause very small text.
left
Default TRUE, meaning the left side of a split is the path
taken if the split condition is true.
With left=FALSE the split labels are changed so the right side is true.
xflip
Default FALSE. If TRUE, flip the tree horizontally.
yflip
Default FALSE. If TRUE, flip the tree vertically, so the root
is at the bottom.
digits
The number of significant digits in displayed numbers.
Default 2.
If 0, use getOption("digits").
If negative, use the standard format function
(with the absolute value of digits).
When digits is positive, the following details apply:
Numbers from 0.001 to 9999 are printed without an exponent
(and the number of digits is actually only a suggestion,
see format for details).
Numbers out that range are printed with an “engineering” exponent (a multiple of 3).
varlen
Length of variable names in text at the splits
(and, for class responses, the class in the node label).
Default -8, meaning truncate to eight characters.
Possible values:
0 use full names.
greater than 0 call abbreviate with the given varlen.
less than 0 truncate variable names to the shortest length where they are still unique,
but never truncate to shorter than abs(varlen).
faclen
Length of factor level names in splits.
Default 3, meaning abbreviate to three characters.
Possible values are as varlen above, except that
for back-compatibility with text.rpart the special value 1
means represent the factor levels with alphabetic characters
(a for the first level, b for the second, etc.).
roundint
If roundint=TRUE (default) and all values of a predictor in the
training data are integers, then splits for that predictor
are rounded to integer.
For example, display nsiblings < 3 instead of nsiblings < 2.5.
If roundint=TRUE and the data used to build the model is no longer
available, a warning will be issued.
Using roundint=FALSE is advised if non-integer values are in fact possible
for a predictor, even though all values in the training data for that
predictor are integral.
cex
Default NULL, meaning calculate the text size automatically.
Since font sizes are discrete, the cex you ask for
may not be exactly the cex you get.
tweak
Adjust the (possibly automatically calculated) cex.
Using tweak is often easier than specifying cex.
The default tweak is 1, meaning no adjustment.
Use say tweak=1.2 to make the text 20% larger.
Since font sizes are discrete,
a small change to tweak may not actually change the type size,
or change it more than you want.
clip.facs
Default FALSE.
If TRUE, print splits on factors as female instead of
sex = female; the variable name and equals is dropped.
Another example: print survived or died rather than
survived = survived or survived = died.
clip.right.labs
Applies only if type=3 or 4.
Default is TRUE meaning “clip” the right-hand split labels,
i.e., don't print variable=.
See also clip.left.labs.
compress
If TRUE (the default), make more space
by shifting nodes horizontally where space is available.
This often allows larger text.
(This is the same as plot.rpart's argument of the same name,
except that here the default is TRUE.)
ycompress
If TRUE (the default unless uniform=FALSE),
make more space by shifting labels vertically where space is available.
Actually, this only kicks in
if the initial automatically calculated cex is less than 0.7.
Use ycompress=FALSE if you feel the resulting display is too messy.
In the current implementation, the shifting algorithm
works a little better (allowing larger text)
with type=1, 2, or 3.
Margin
Extra white space around the tree, as a fraction of the graph width.
Default 0, meaning no extra space.
To add say 10% space around the tree use Margin=0.1.
(This is the margin argument of plot.rpart.
The name was changed to prevent partial matching with mar,
which can be passed in as a ... argument.)
space
Horizontal space to the box border on each side of the node label text,
in character widths.
Default 1.
Use this (and yspace) for bigger boxes.
Since this affects the size of the (possibly invisible) boxes,
it also affects the graph layout and hence also the automatic calculation of cex.
gap
Minimum horizontal gap between the (possibly invisible) boxes, in character widths.
Default NULL, meaning automatically choose a suitable value
(normally 1, but if the graph is very crowded will be set to 0,
permitting boxes to touch to allow a bigger cex).
See also space.
snip
Default FALSE.
Set TRUE to interactively trim the tree with the mouse.
See the package vignette (or just try it).
snip.fun
Function invoked after each mouse click when snip=TRUE.
Default NULL, meaning no function.
Otherwise set snip.fun to your own function
with the prototype function(tree), where tree is the snipped tree.
See the package vignette for an example.
The following control the node labels.
trace
Default FALSE.
Use TRUE to print the automatically calculated cex, xlim, and ylim.
Use integer values greater than 1 for more detailed tracing.
box.col
Color of the boxes around the text.
Default 0, meaning use the background color.
If this argument is used, the box.palette argument is ignored.
box.palette
Palette for coloring the node boxes based on the fitted value.
This is a vector of colors,
for example box.palette=c("green", "green2", "green4").
Small fitted values are displayed with colors at the start of the vector;
large values with colors at the end.
Quantiles are used to partition the fitted values.
The special value box.palette=0 (default for prp) uses
the background color (typically white).
The special value box.palette="auto" (default for
rpart.plot, case insensitive) automatically selects a
predefined palette based on the type of model.
Otherwise specify a predefined palette
e.g. box.palette="Grays" for the predefined gray palette (a range of grays).
The predefined palettes are (see the show.prp.palettes function):
Grays Greys Greens Blues Browns Oranges Reds Purples
Gy Gn Bu Bn Or Rd Pu (alternative names for the above palettes)
BuGn GnRd BuOr etc. (two-color diverging palettes: any combination of two of the above palettes)
RdYlGn GnYlRd BlGnYl YlGnBl (three color palettes)
Prefix the palette name with "-" to reverse the order of the colors
e.g. box.palette="-auto" or box.palette="-Grays".
The box.palette argument is ignored if the box.col palette argument is specified.
pal.thresh
Applies when box.palette is a
two-color diverging palette (such as BuGn).
Specifies the response threshold to split the two sub-palettes (such as
Bu and Gn).
For example, to display fitted values less than 90 in shades of blue
and values greater than 90 in shades of green, use
pal.thresh=90 with box.palette="BuGn".
By default pal.thresh is calculated automatically.
(For a two-class response the default threshold is 0.5; for
a continuous response the default is the median fitted value.)
Node boxes for fitted values less than the threshold are displayed using
colors from the first sub-palette;
boxes for fitted values greater than the threshold are displayed using
colors from the second sub-palette.
This argument is ignored if box.palette isn't a two-color diverging palette,
and is ignored for models with multiple-class responses (more than two classes).
pal.node.fun
Specifies how the box.palette argument is handled when
the node.fun argument is specified.
Default is FALSE, meaning ignore node.fun and use
the fitted value to select the node color from box.palette as usual.
If TRUE, use the label returned by the node
function (instead of the fitted value) to select the color.
The first number in each label returned by the node function is used,
skipping over any non-numeric initial text in the label.
An error message will be issued if a label doesn't include a number.
This argument is ignored if node.fun isn't specified,
and is ignored for models with multiple-class responses (more than two
classes).
border.col
Color of the box border around the text.
Default col, the color of the text in the box.
Use 0 for no border.
(Note: par settings like col can be passed in as ... arguments.
If not passed in, par("col") is used.)
round
Controls the rounding of the corners of the node boxes.
Default NULL, meaning calculate automatically.
Else specify 0 for sharp edges, and values greater
than 0 for rounded edges.
Bigger is more round.
Values too big for the size of the box get silently reduced.
leaf.round
Controls the rounding of the corners of the leaf node boxes.
Default NULL, meaning use round.
Else specify a value greater than or equal to 0.
shadow.col
Color of the shadow under the boxes.
Default 0, no shadow.
Try "gray" or "darkgray".
(Note: overlapping shadows look better on devices that support alpha channels.
If you get the message "Warning: semi-transparency is not supported" please let me know –
it means that a fix is needed to the code that determines if the device supports alpha channels.)
prefix
Default "".
Prepend this string to the node labels.
So could be the name of the fitted response, for instance.
suffix
Default "".
Append this string to the node labels.
Text after a double newline "\n\n" (if any) will be plotted under the box.
(Actually, double newlines can be used in any of the prefix or suffix
arguments for this purpose.)
xsep
String which separates the individual counts and probabilities
in node labels when extra>0.
Default NULL meaning automatically select: usually
" " (two spaces), but " / " for rates.
Use xsep="/" for compatibility with text.rpart.
See also facsep, which separates the factor levels in split labels.
under.percent
Control whitespace before the percentage (when 100 is used with the extra argument).
One of
0 put a space before the percentage
1 put a newline before the percentage
2 (default) automatically choose a space or newline before the percentage.
The following control the text under the boxes (apply only if
under=TRUE or there is a double newline \n\n in prefix or suffix).
under.font
Font of the text under the box. Default font (which can be passed in as a ... argument).
under.col
Color of the text under the box.
Default 1.
under.cex
Size of the text under the box relative to the text in the box.
Default .8, smaller than the text in the box.
The following control the split labels.
split.cex
Size of the split text relative to cex
(which by default is calculated automatically).
Default 1.
split.font
Font for the split labels.
Default 2, bold.
(Note: use font to change the node label text.)
split.family
Font family for the split labels.
Default "",
or use something like split.family="serif".
(Note: use family to change the node label text.)
split.col
Color of the split label text.
Default 1.
(Note: use col to change the node label text.)
split.box.col
Color of the split boxes.
Default 0, meaning use the background color.
split.border.col
Color of the split box borders.
Default 0, invisible.
split.lty
Line type for the split box borders.
The default is 1, but the border will be invisible
unless you change the default split.border.col.
(Note: use lty to change the node box borders.)
split.lwd
Line width of the split box border relative to cex
(which by default is calculated automatically).
The border is by default invisible, see split.border.col.
split.round
Controls the rounding of the corners of the split boxes.
Default 0, meaning sharp corners.
Else specify a value greater than or equal to 0.
The split boxes are by default invisible,
see split.box.col and split.border.col).
split.shadow.col
Color of the shadow under the split boxes.
Default 0, no shadow.
split.prefix
Default "".
Prepend this string to the split labels.
right.split.prefix
Default split.prefix.
Prepend this string to the right split labels.
Applies only when type=3 or 4.
split.suffix
Default "".
Append this string to the split labels.
right.split.suffix
Default split.suffix.
Append this string to the right split labels.
Applies only when type=3 or 4.
facsep
Default ",".
String which separates the factor levels in split labels.
See also xsep, which separates the individual counts when extra is used.
eq
Default " = ".
String which separates the factor name from the levels in split labels.
The idea is that you can add or remove spaces around the =, or use
words if that suits you.
lt
Default " < ".
String which represents “less than” in split labels.
ge
Default " >= ".
String which represents “greater than or equal” in split labels.
The following control the branches.
branch.col
Color of the branch lines.
Default 1, but set to "gray" if branch.type is nonzero.
branch.lty
Branch line type.
Default 1.
branch.lwd
Line width of the branch lines relative to cex
(which by default is calculated automatically).
(Note: branch.lwd does not control the width of the
“wide branches” drawn when branch.type is nonzero.)
branch.type
Default 0.
If nonzero draw “wide branches”, with branch widths proportional
to the parameter selected by branch.type as follows:
0 The default. The branch lines are drawn conventionally.
1 deviance
2 sqrt(deviance)
3 deviance / nobs
4 sqrt(deviance / nobs) (the standard deviation when method="anova")
5 weight (frame$wt).
This is the number of observations at the node,
unless rpart's weight argument was used.
6 complexity
7 abs(predicted value)
8 predicted value - min(predicted value)
9 constant (for checking visual perception of the
relative width of branches).
Otherwise set branch.type to your own function.
The function should take a single argument x
(the rpart object) and return
a numeric vector of non-negative widths corresponding to rows in frame.
See get.branch.widths in the source code.
Note: with a nonzero branch.type, in the current implementation
the branch argument will be silently changed to 1
(if branch > .5) or 0 (if branch < .5)
branch.tweak
Default 1.
Applies only if branch.type is nonzero.
Use this argument to scale the widths of the branches,
for example, branch.tweak=.5 to halve the width of the branches.
(By default, prp normalizes the widths so the
widest branch is one-fifth the plot width.)
min.branch.width
Default 0.002.
Applies only if branch.type is nonzero.
The minimum width of a branch, as a fraction of the page width.
The width of branches that would be thinner than min.branch.width is clamped.
Increase min.branch.width if the thinnest branches are too skinny on your display device.
branch.fill
Color used to fill the wide branch lines.
Applies only if branch.type is nonzero.
Default branch.col.
The following control the node numbers (with nn=TRUE).
nn.cex
Default NULL, meaning calculate the cex
of the node numbers automatically.
This and the following arguments apply only when nn=TRUE.
nn.font
Font for the node numbers.
Default 3, italic.
nn.family
Font family for the node numbers.
Default "".
nn.col
Color of the node number text.
Default 1.
nn.box.col
Color of the boxes around the node numbers.
Default 0, meaning use the background color.
nn.border.col
Color of the box border around the node numbers.
Default nn.col.
nn.lty
Line type of the node number box border.
Default 1.
nn.lwd
Line width of the node box border relative to cex
(which by default is calculated automatically).
Default NULL, meaning use lwd (which can be passed in as a ... argument).
nn.round
Controls the rounding of the corners of the node number boxes.
Default .3, meaning small corners.
Else specify a value greater than or equal to 0.
yes.text, no.text
Text displayed when yesno=TRUE.
Default yes.text="yes" and no.text="no".
The following are user definable functions.
node.fun
The function that generates the text at the node labels.
The default is NULL,
which means use a default function internal to prp.
(This is necessary for full support of extra as described
in the section on extra above.)
Otherwise set node.fun to your own function
with the prototype
function(x, labs, digits, varlen)
See the package vignette for details.
See also the pal.node.fun argument.
split.fun
The function that generates the text at the splits.
The default is NULL,
which means use a default function internal to prp.
Otherwise set split.fun to your own function with the
prototype function(x, labs, digits, varlen, faclen)
FUN
The function that displays the text on the screen.
Default text.
The following are esoteric parameters, mostly for the graph layout engine.
nspace
Applies only when compress=TRUE.
Default nspace=branch.
The size of the space between a split and a leaf, relative to
the space between leaves.
minbranch
Applies only when uniform=FALSE. Default .3.
The minimum height between levels is clamped at
minbranch times the mean interlevel distance.
Needed because sometimes a split gives little or no improvement in deviance, and
an interlevel distance strictly proportional to the improvement would
leave no room for the label.
do.par
Default TRUE, meaning adjust the mar parameter
so the tree fills the figure region.
This also sets xpd=NA.
These graphic parameters are restored to their original
state before prp exits.
If you explicitly set mar or xpd, prp will
use your setting regardless of the setting of do.par.
add.labs
Default TRUE, meaning display the labels.
If FALSE, gives a bare bones display similar to plot.rpart.
clip.left.labs
Like clip.right.labs but for the left labels.
Default is FALSE.
Note that clip.left.labs and clip.right.labs can be vectors,
indexed on the split number.
fam.main
Font family for the main text. Default "".
The (inconsistent) name was chosen to minimize partial matching
with main and family which can be passed in as
in as ... arguments.
yshift
Vertical position of the labels, in character heights relative to their default position.
Default 0.
Negative values move the text down; positive up
(the box around the text will follow along).
yspace
Vertical space to the box border above and below the node label text, in character heights.
Default space.
See the comments for space.
shadow.offset
Offset of the shadow from the boxes, in character widths.
Default .4
(but the shadow will be invisible unless the default shadow.col is changed).
split.adj
Horizontal position of the split text.
In string width units, as is the convention for adj arguments.
Default NULL, meaning use adj
(which defaults to 0.5 but can be passed in as a ... argument).
Use values less/more than .5 to shift the text left/right
(the box around the text will follow along).
split.yshift
Vertical position of the split labels,
in character heights relative to their default positions.
Default 0.
Negative values move the text down; positive up
(the box around the text will follow along).
This adjusts the positions of the split labels relative to the node labels.
(Use yshift if you want to shift both the split and node labels.)
split.space
Horizontal space between the split label text and the box,
in character widths.
Default space.
Affects the size of the box drawn around the text.
The split boxes are by default invisible
(see split.box.col and split.border.col),
but nevertheless affect the graph layout used
in the automatic calculation of cex.
split.yspace
Vertical space between the split label text and the box, in character heights.
Default yspace.
split.shadow.offset
Offset of the shadow from the split boxes, in character widths.
Default shadow.offset.
(but the shadow will be invisible unless the default shadow.col is changed).
nn.adj
Horizontal position of the node label text.
Default .5.
nn.yshift
Vertical position of the node numbers, in character heights relative to their default positions.
Default 0.
nn.space
Horizontal space to the box border on each side of the node number text,
in character widths.
Default .8.
nn.yspace
Vertical space to the box border above and below the node number text, in character heights.
Default .5.
under.ygap
Applies if text is plotted under the box
(i.e. if under=TRUE or there is a double newline in prefix or suffix).
Vertical gap (in char heights) between the lower edge of the box and
the top of the text under the box.
yesno.yshift
Vertical position of "yes" and "no"
in character heights relative to their default position.
Default 0.
Applies only when yesno=TRUE.
ygap
Minimum vertical gap between boxes, in character heights.
Default gap/2.
xcompact
If TRUE (the default) and there is too much white space,
automatically change xlim to compact the entire tree horizontally.
This usually only activates for small trees.
(The xcompact and ycompact arguments compact the tree as a whole,
whereas the compress and ycompress arguments move parts of the tree
into available space.)
ycompact
If TRUE (the default) and there is too much vertical space,
automatically change ylim to compact the entire tree vertically.
xcompact.ratio
Default .8.
Applies only when xcompact=TRUE.
The maximum possible without overplotting is 1,
but compacting by .8 usually
gives more pleasing spacing (it gives more space).
min.inter.height
Default 4.
Applies only when ycompact=TRUE.
Minimum height (in units of character height)
between the lowest label in a layer and the highest label in the layer below it.
max.auto.cex
Clamp the maximum automatically calculated cex at this value
Default 1, meaning never expand cex, only contract when necessary.
min.auto.cex
Default .15.
Never downscale to less than this when automatically calculating cex,
even if overplotted labels result.
(The graph layout algorithm is unstable with cex's below 0.15
– meaning that the automatic type size may be smaller than necessary.)
ycompress.cex
Default .7.
Applies only when ycompress=TRUE.
Apply the ycompress algorithm if the initial automatically calculated cex is less than this.
The idea is that we don't want to shift if we get an acceptable cex without shifting.
Make Inf to always attempt shifting.
accept.cex
Accept shifting only if it causes at least this much improvement in cex
(because we don't want to shift if it gives only a small improvement in cex).
Default 1.1 i.e. require at least a 10% improvement.
Use 0 to always accept shifts and
Inf to never accept (or use ycompress=FALSE).
shift.amounts
Default c(1.5, 2, 3).
For ycompress, choose the best cex yielded
by shifting nodes by these amounts,
in multiples of the box heights (after initial scaling).
Fallen.yspace
Extra space for fallen leaves.
Default .1, meaning allow 10% of the vertical space for the fallen leaves.
(The name Fallen.yspace uses upper case to avoid partial matching with fallen.leaves.)
boxes.include.gap
Default FALSE.
Include gap and ygap when drawing the boxes, for debugging purposes.
(To draw the boxes, see
box.col, border.col, split.box.col, and split.border.col.)
This argument only affects the way the boxes are drawn, not the graph layout algorithm in any way.
With the optimum cex at least one pair of boxes displayed in this manner will just touch
(but none will overlap).
legend.x
Applies only to models with a multilevel class response
(not binary or anova models, for which no legend is drawn).
Horizontal position of the legend.
Typically a value between 0 and 1, although values beyond
those limits are often useful.
Default is NULL meaning automatically position the legend (assuming
there is enough space). Use NA for no legend.
Use trace=TRUE to see the automatically calculated legend position.
legend.y
Like legend.x but for the vertical position of the legend.
legend.cex
Like legend.x but for the relative size of the legend text.
Default is 1.
...
Extra par arguments. Only the “important” par arguments are supported.
Note that arguments like col apply only to the node labels.
To affect the split labels or branch lines, use split.col and branch.col instead.
Value
A list with the following components.
With the default args most of these are calculated automatically.
obj
The rpart object.
Identical to the x argument passed in unless snip was used.
snipped.nodes
The snipped nodes, NULL unless snip was used.
xlim, ylim
The graph limits.
x, y
The node coords.
branch.x, branch.y
The branch line coords.
labs
The node labels.
cex
The node label cex.
boxes
The coords of the boxes around the nodes.
split.labs
The split labels.
split.cex
The split label cex.
split.boxes
The coords of the boxes around the splits.
See Also
The package vignette Plotting rpart trees with the rpart.plot package
rpart.plot
Functions in the rpart package:
plot.rpart
text.rpart
rpart
Examples
data(ptitanic)
tree <- rpart(survived ~ ., data = ptitanic, cp = .02)
# cp = .02 because want small tree for demo
old.par <- par(mfrow = c(2,2))
# put 4 figures on one page
prp(tree, main = "default prp\n(type = 0, extra = 0)")
prp(tree, main = "type = 4, extra = 6\nbox.palette = \"auto\"",
type = 4, extra = 6, # label all nodes, show prob of second class
box.palette = "auto", # auto color the nodes based on the model type
faclen = 0) # faclen = 0 to print full factor names
cols <- ifelse(tree$frame$yval == 1, "darkred", "green4")
# green if survived
prp(tree, main = "assorted arguments",
extra = 106, # display prob of survival and percent of obs
nn = TRUE, # display the node numbers
fallen.leaves = TRUE, # put the leaves on the bottom of the page
shadow.col = "gray", # shadows under the leaves
branch.lty = 3, # draw branches using dotted lines
branch = .5, # change angle of branch lines
faclen = 0, # faclen = 0 to print full factor names
trace = 1, # print the auto calculated cex, xlim, ylim
split.cex = 1.2, # make the split text larger than the node text
split.prefix = "is ", # put "is " before split text
split.suffix = "?", # put "?" after split text
col = cols, border.col = cols, # green if survived
split.box.col = "lightgray", # lightgray split boxes (default is white)
split.border.col = "darkgray", # darkgray border on split boxes
split.round = .5) # round the split box corners a tad
# compare to the plotting functions in the rpart package
plot(tree, uniform = TRUE, compress = TRUE, branch = .2)
text(tree, use.n = TRUE, cex = .8, xpd = NA) # cex is a guess, depends on your window size
title("compare to the plotting functions\nin the rpart package", cex.sub = .8)
par(old.par)
rpart.plot documentation built on May 29, 2024, 12:07 p.m.
R Package Documentation
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| prp | R Documentation |
Plot an rpart model.
Description
Plot an rpart model.
First-time users should use rpart.plot instead,
which provides a simplified interface to this function.
For an overview, please see the package vignette Plotting rpart trees with the rpart.plot package.
The arguments of this function are a superset of those of
rpart.plot and some of the arguments have different
defaults.
In detail the different defaults are:
| | | rpart.plot | | | prp | | | |
type | | | 2 | | | 0 | | |
extra | | | "auto" | | | 0 | | |
fallen.leaves | | | TRUE | | | FALSE | | |
varlen | | | 0 | | | -8 | | |
faclen | | | 0 | | | 3 | | |
box.palette | | | "auto" | | | 0 | | |
The defaults are different for historical reasons: for backwards
compatibility the defaults of prp haven't changed,
whereas the defaults of rpart.plot were changed when
type="auto" and box.palette were introduced
in version 2.0.0 of this package.
Usage
prp(x=stop("no 'x' arg"),
type=0, extra=0, under=FALSE, fallen.leaves=FALSE,
nn=FALSE, ni=FALSE, yesno=TRUE,
branch=if(fallen.leaves) 1 else .2,
uniform=TRUE, left=TRUE, xflip=FALSE, yflip=FALSE,
digits=2, varlen=-8, faclen=3, roundint=TRUE,
cex=NULL, tweak=1,
clip.facs=FALSE, clip.right.labs=TRUE,
compress=TRUE, ycompress=uniform,
Margin=0, space=1, gap=NULL,
snip=FALSE, snip.fun=NULL, trace=FALSE,
box.col=0, box.palette=0,
pal.thresh=NULL, pal.node.fun=FALSE,
border.col=col,
round=NULL, leaf.round=NULL,
shadow.col=0, prefix="", suffix="", xsep=NULL,
under.percent=2, under.font=font, under.col=1, under.cex=.8,
split.cex=1, split.font=2, split.family=family, split.col=1,
split.box.col=0, split.border.col=0,
split.lty=1, split.lwd=NULL, split.round=0,
split.shadow.col=0,
split.prefix="", right.split.prefix=NULL,
split.suffix="", right.split.suffix=NULL,
facsep=",", eq=" = ", lt=" < ", ge=" >= ",
branch.col=if(is.zero(branch.type)) 1 else "gray",
branch.lty=1, branch.lwd=NULL,
branch.type=0, branch.tweak=1,
min.branch.width=.002, branch.fill=branch.col,
nn.cex=NULL, nn.font=3, nn.family="", nn.col=1,
nn.box.col=0, nn.border.col=nn.col,
nn.lty=1, nn.lwd=NULL, nn.round=.3,
yes.text="yes", no.text="no",
node.fun=NULL,
split.fun=NULL,
FUN="text",
nspace=branch, minbranch=.3, do.par=TRUE,
add.labs=TRUE, clip.left.labs=(type == 5), fam.main="",
yshift=0, yspace=space, shadow.offset=.4,
split.adj=NULL, split.yshift=0, split.space=space,
split.yspace=yspace, split.shadow.offset=shadow.offset,
nn.adj=.5, nn.yshift=0, nn.space=.8, nn.yspace=.5,
ygap=gap/2, under.ygap=.5, yesno.yshift=0,
xcompact=TRUE, ycompact=uniform, xcompact.ratio=.8, min.inter.height=4,
max.auto.cex=1, min.auto.cex=.15, ycompress.cex=.7, accept.cex=1.1,
shift.amounts=c(1.5, 2),
Fallen.yspace=.1, boxes.include.gap=FALSE,
legend.x=NULL, legend.y=NULL, legend.cex=1,
...)
Arguments
x |
An |
type |
Type of plot. Possible values: 0 Default. Draw a split label at each split and a node label at each leaf. 1 Label all nodes, not just leaves.
Similar to 2 Like 3 Draw separate split labels for the left and right directions. 4 Like 5 Show the split variable name in the interior nodes. |
extra |
Display extra information at the nodes. Possible values: "auto" (case insensitive) 0 Default. No extra information. 1 Display the number of observations that fall in the node
(per class for 2 Class models: display the classification rate at the node,
expressed as the number of correct classifications and the number
of observations in the node. 3 Class models: misclassification rate at the node, expressed as the number of incorrect classifications and the number of observations in the node. 4 Class models: probability per class of observations in the node (conditioned on the node, sum across a node is 1). 5 Class models:
like 6 Class models: the probability of the second class only. Useful for binary responses. 7 Class models:
like 8 Class models: the probability of the fitted class. 9 Class models: The probability relative to all observations – the sum of these probabilities across all leaves is 1. This is in contrast to the options above, which give the probability relative to observations falling in the node – the sum of the probabilities across the node is 1. 10 Class models:
Like 11 Class models:
Like +100 Add Note: Unlike |
under |
Applies only if |
fallen.leaves |
Default |
nn |
Display the node numbers.
Default |
ni |
Display the node indices,
i.e. the row numbers of the nodes in the object's |
yesno |
One of |
branch |
Controls the shape of the branch lines.
Specify a value between |
uniform |
If |
left |
Default |
xflip |
Default |
yflip |
Default |
digits |
The number of significant digits in displayed numbers.
Default |
varlen |
Length of variable names in text at the splits
(and, for class responses, the class in the node label).
Default 0 use full names. greater than 0 call less than 0 truncate variable names to the shortest length where they are still unique,
but never truncate to shorter than |
faclen |
Length of factor level names in splits.
Default |
roundint |
If |
cex |
Default |
tweak |
Adjust the (possibly automatically calculated) |
clip.facs |
Default |
clip.right.labs |
Applies only if |
compress |
If |
ycompress |
If |
Margin |
Extra white space around the tree, as a fraction of the graph width.
Default |
space |
Horizontal space to the box border on each side of the node label text,
in character widths.
Default |
gap |
Minimum horizontal gap between the (possibly invisible) boxes, in character widths.
Default |
snip |
Default |
snip.fun |
Function invoked after each mouse click when The following control the node labels. |
trace |
Default |
box.col |
Color of the boxes around the text.
Default |
box.palette |
Palette for coloring the node boxes based on the fitted value.
This is a vector of The special value The special value Otherwise specify a predefined palette
e.g. Prefix the palette name with The |
pal.thresh |
Applies when |
pal.node.fun |
Specifies how the |
border.col |
Color of the box border around the text.
Default |
round |
Controls the rounding of the corners of the node boxes.
Default |
leaf.round |
Controls the rounding of the corners of the leaf node boxes.
Default |
shadow.col |
Color of the shadow under the boxes.
Default |
prefix |
Default |
suffix |
Default |
xsep |
String which separates the individual counts and probabilities
in node labels when |
under.percent |
Control whitespace before the percentage (when 100 is used with the The following control the text under the boxes (apply only if
|
under.font |
Font of the text under the box. Default |
under.col |
Color of the text under the box.
Default |
under.cex |
Size of the text under the box relative to the text in the box.
Default The following control the split labels. |
split.cex |
Size of the split text relative to |
split.font |
Font for the split labels.
Default |
split.family |
Font family for the split labels. |
split.col |
Color of the split label text.
Default |
split.box.col |
Color of the split boxes.
Default |
split.border.col |
Color of the split box borders.
Default |
split.lty |
Line type for the split box borders.
The default is |
split.lwd |
Line width of the split box border relative to |
split.round |
Controls the rounding of the corners of the split boxes.
Default |
split.shadow.col |
Color of the shadow under the split boxes.
Default |
split.prefix |
Default |
right.split.prefix |
Default |
split.suffix |
Default |
right.split.suffix |
Default |
facsep |
Default |
eq |
Default |
lt |
Default |
ge |
Default The following control the branches. |
branch.col |
Color of the branch lines.
Default |
branch.lty |
Branch line type.
Default |
branch.lwd |
Line width of the branch lines relative to |
branch.type |
Default 0 The default. The branch lines are drawn conventionally. Otherwise set Note: with a nonzero |
branch.tweak |
Default |
min.branch.width |
Default |
branch.fill |
Color used to fill the wide branch lines.
Applies only if The following control the node numbers (with |
nn.cex |
Default |
nn.font |
Font for the node numbers.
Default |
nn.family |
Font family for the node numbers.
Default |
nn.col |
Color of the node number text.
Default |
nn.box.col |
Color of the boxes around the node numbers.
Default |
nn.border.col |
Color of the box border around the node numbers.
Default |
nn.lty |
Line type of the node number box border.
Default |
nn.lwd |
Line width of the node box border relative to |
nn.round |
Controls the rounding of the corners of the node number boxes.
Default |
yes.text, no.text |
Text displayed when The following are user definable functions. |
node.fun |
The function that generates the text at the node labels.
The default is |
split.fun |
The function that generates the text at the splits.
The default is |
FUN |
The function that displays the text on the screen.
Default The following are esoteric parameters, mostly for the graph layout engine. |
nspace |
Applies only when |
minbranch |
Applies only when |
do.par |
Default |
add.labs |
Default |
clip.left.labs |
Like |
fam.main |
Font family for the main text. Default |
yshift |
Vertical position of the labels, in character heights relative to their default position.
Default |
yspace |
Vertical space to the box border above and below the node label text, in character heights.
Default |
shadow.offset |
Offset of the shadow from the boxes, in character widths.
Default |
split.adj |
Horizontal position of the split text.
In string width units, as is the convention for |
split.yshift |
Vertical position of the split labels,
in character heights relative to their default positions.
Default |
split.space |
Horizontal space between the split label text and the box,
in character widths.
Default |
split.yspace |
Vertical space between the split label text and the box, in character heights.
Default |
split.shadow.offset |
Offset of the shadow from the split boxes, in character widths.
Default |
nn.adj |
Horizontal position of the node label text.
Default |
nn.yshift |
Vertical position of the node numbers, in character heights relative to their default positions.
Default |
nn.space |
Horizontal space to the box border on each side of the node number text,
in character widths.
Default |
nn.yspace |
Vertical space to the box border above and below the node number text, in character heights.
Default |
under.ygap |
Applies if text is plotted under the box
(i.e. if |
yesno.yshift |
Vertical position of "yes" and "no"
in character heights relative to their default position.
Default |
ygap |
Minimum vertical gap between boxes, in character heights.
Default |
xcompact |
If |
ycompact |
If |
xcompact.ratio |
Default |
min.inter.height |
Default |
max.auto.cex |
Clamp the maximum automatically calculated |
min.auto.cex |
Default |
ycompress.cex |
Default |
accept.cex |
Accept shifting only if it causes at least this much improvement in |
shift.amounts |
Default |
Fallen.yspace |
Extra space for fallen leaves.
Default |
boxes.include.gap |
Default |
legend.x |
Applies only to models with a multilevel class response
(not binary or anova models, for which no legend is drawn). |
legend.y |
Like |
legend.cex |
Like |
... |
Extra |
Value
A list with the following components. With the default args most of these are calculated automatically.
obj |
The |
snipped.nodes |
The snipped nodes, |
xlim, ylim |
The graph limits. |
x, y |
The node coords. |
branch.x, branch.y |
The branch line coords. |
labs |
The node labels. |
cex |
The node label |
boxes |
The coords of the boxes around the nodes. |
split.labs |
The split labels. |
split.cex |
The split label |
split.boxes |
The coords of the boxes around the splits. |
See Also
The package vignette Plotting rpart trees with the rpart.plot package
rpart.plot
Functions in the rpart package:
plot.rpart
text.rpart
rpart
Examples
data(ptitanic)
tree <- rpart(survived ~ ., data = ptitanic, cp = .02)
# cp = .02 because want small tree for demo
old.par <- par(mfrow = c(2,2))
# put 4 figures on one page
prp(tree, main = "default prp\n(type = 0, extra = 0)")
prp(tree, main = "type = 4, extra = 6\nbox.palette = \"auto\"",
type = 4, extra = 6, # label all nodes, show prob of second class
box.palette = "auto", # auto color the nodes based on the model type
faclen = 0) # faclen = 0 to print full factor names
cols <- ifelse(tree$frame$yval == 1, "darkred", "green4")
# green if survived
prp(tree, main = "assorted arguments",
extra = 106, # display prob of survival and percent of obs
nn = TRUE, # display the node numbers
fallen.leaves = TRUE, # put the leaves on the bottom of the page
shadow.col = "gray", # shadows under the leaves
branch.lty = 3, # draw branches using dotted lines
branch = .5, # change angle of branch lines
faclen = 0, # faclen = 0 to print full factor names
trace = 1, # print the auto calculated cex, xlim, ylim
split.cex = 1.2, # make the split text larger than the node text
split.prefix = "is ", # put "is " before split text
split.suffix = "?", # put "?" after split text
col = cols, border.col = cols, # green if survived
split.box.col = "lightgray", # lightgray split boxes (default is white)
split.border.col = "darkgray", # darkgray border on split boxes
split.round = .5) # round the split box corners a tad
# compare to the plotting functions in the rpart package
plot(tree, uniform = TRUE, compress = TRUE, branch = .2)
text(tree, use.n = TRUE, cex = .8, xpd = NA) # cex is a guess, depends on your window size
title("compare to the plotting functions\nin the rpart package", cex.sub = .8)
par(old.par)
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