Plot the distribution of the predicted values for each class.
Can be used for earth models, but also for models built by
lm,
glm,
lda,
etc.
plotd(object, hist = FALSE, type = NULL, nresponse = NULL, dichot = FALSE,
trace = FALSE, xlim = NULL, ylim = NULL, jitter = FALSE, main=NULL,
xlab = "Predicted Value", ylab = if(hist) "Count" else "Density",
lty = 1, col = c("gray70", 1, "lightblue", "brown", "pink", 2, 3, 4),
fill = if(hist) col[1] else 0,
breaks = "Sturges", labels = FALSE,
kernel = "gaussian", adjust = 1, zero.line = FALSE,
legend = TRUE, legend.names = NULL, legend.pos = NULL,
cex.legend = .8, legend.bg = "white", legend.extra = FALSE,
vline.col = 0, vline.thresh = .5, vline.lty = 1, vline.lwd = 1,
err.thresh = vline.thresh, err.col = 0, err.border = 0, err.lwd = 1,
xaxt = "s", yaxt = "s", xaxis.cex = 1, sd.thresh = 0.01, ...)To start off, look at the arguments object, hist, type.
For predict methods with multiple column responses, see the nresponse argument.
For factor responses with more than two levels, see the dichot argument.
Model object. Typically a model which predicts a class or a class discriminant.
FALSE (default) to call density internally.
TRUE to call hist internally.
Type parameter passed to predict.
For allowed values see the predict method for
your object (such as predict.earth).
By default, plotd tries to automatically select a suitable
value for the model in question.
(This is "response" for all objects except rpart models, where "vector"
is used. The choices will often be inappropriate.)
Typically you would set hist=TRUE when type="class".
Which column to use when predict returns multiple columns.
This can be a column index or column name
(which may be abbreviated, partial matching is used).
The default is NULL, meaning use all columns of the predicted response.
Dichotimise the predicted response.
This argument is ignored except for models where the observed response
is a factor with more than two levels
and the predicted response is a numeric vector.
The default FALSE separates the response into a group for each factor.
With dichot=TRUE the response is separated into just two groups:
the first level of the factor versus the remaining levels.
Default FALSE.
Use TRUE or 1 to trace plotd ---
useful to see how plotd
partitions the predicted response into classes.
Use 2 for more details.
Limits of the x axis.
The default NULL means determine these limits automatically,
else specify c(xmin,xmax).
Limits of the y axis.
The default NULL means determine these limits automatically,
else specify c(ymin,ymax).
Jitter the histograms or densities horizontally to minimize overplotting.
Default FALSE.
Specify TRUE to automatically calculate the jitter,
else specify a numeric jitter value.
Main title. Values:
"string" string
"" no title
NULL (default) generate a title from the call.
x axis label.
Default is "Predicted Value".
y axis label.
Default is if(hist) "Count" else "Density".
Per class line types for the plotted lines. Default is 1 (which gets recycled for all lines).
Per class line colors. The first few colors of the default are intended to be easily distinguishable on both color displays and monochrome printers.
Fill color for the plot for the first class.
For hist=FALSE, the default is 0, i.e., no fill.
For hist=TRUE, the default is the first element in the col argument.
Passed to hist.
Only used if hist=TRUE.
Default is "Sturges".
When type="class", setting breaks to a low number
can be used to widen the histogram bars
TRUE to draw counts on the hist plot.
Only used if hist=TRUE.
Default is FALSE.
Passed to density.
Only used if hist=FALSE.
Default is "gaussian".
Passed to density.
Only used if hist=FALSE.
Default is 1.
Passed to plot.density.
Only used if hist=FALSE.
Default is FALSE.
TRUE (default) to draw a legend, else FALSE.
Class names in legend.
The default NULL means determine these automatically.
Position of the legend.
The default NULL means position the legend automatically,
else specify c(x,y).
cex for legend.
Default is .8.
bg color for legend.
Default is "white".
Show (in the legend) the number of occurrences of each class.
Default is FALSE.
Horizontal position of optional vertical line.
Default is 0.5.
The vertical line is intended to indicate class separation.
If you use this, don't forget to set vline.col.
Color of vertical line. Default is 0, meaning no vertical line.
Line type of vertical line.
Default is 1.
Line width of vertical line.
Default is 1.
x axis value specifying the error shading threshold.
See err.col.
Default is vline.thresh.
Specify up to three colors to shade the "error areas" of the density plot.
The default is 0, meaning no error shading.
This argument is ignored unless hist=FALSE.
If there are more than two classes, err.col uses only the first two.
This argument is best explained by running an example:
data(etitanic)
earth.mod <- earth(survived ~ ., data=etitanic)
plotd(earth.mod, vline.col=1, err.col=c(2,3,4))
The three areas are (i) the error area to the left of the threshold,
(ii) the error area to the right of the threshold, and,
(iii) the reducible error area.
If less than three values are specified, plotd re-uses values in a sensible manner.
Use values of 0 to skip areas.
Disjoint regions are not handled well by the current implementation.
Borders around the error shading.
Default is 0, meaning no borders, else specify up to three colors.
Line widths of borders of the error shading.
Default is 1, else specify up to three line widths.
Default is "s".
Use xaxt="n" for no x axis.
Default is "s".
Use yaxt="n" for no y axis.
Only used if hist=TRUE and type="class".
Specify size of class labels drawn on the x axis.
Default is 1.
Minimum acceptable standard deviation for a density.
Default is 0.01.
Densities with a standard deviation less than sd.thresh
will not be plotted (a warning will be issued and the legend
will say "not plotted").
Extra arguments passed to the predict method for the object.
density, plot.density
hist, plot.histogram
earth, plot.earth
if (require(earth)) {
old.par <- par(no.readonly=TRUE);
par(mfrow=c(2,2), mar=c(4, 3, 1.7, 0.5), mgp=c(1.6, 0.6, 0), cex = 0.8)
data(etitanic)
mod <- earth(survived ~ ., data=etitanic, degree=2, glm=list(family=binomial))
plotd(mod)
plotd(mod, hist=TRUE, legend.pos=c(.25,220))
plotd(mod, hist=TRUE, type="class", labels=TRUE, xlab="", xaxis.cex=.8)
par(old.par)
}
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