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Plot Calibration curve
plotCalibration(x, models, times, showPseudo, pseudo.col = NULL,
pseudo.pch = NULL, method = "nne", round = TRUE, bandwidth = NULL,
q = 10, bars = FALSE, hanging = FALSE, names = "quantiles",
showFrequencies = FALSE, jack.density = 55, plot = TRUE, add = FALSE,
diag = !add, legend = !add, axes = !add, xlim = c(0, 1), ylim = c(0,
1), xlab = ifelse(bars, "Risk groups", "Predicted risk"),
ylab = "Observed frequency", col, lwd, lty, pch, type, cause = 1,
percent = TRUE, na.action = na.fail, cex = 1, ...)Object obtained with function Score
Choice of models to plot
Time point specifying the prediction horizon.
If TRUE the pseudo-values are shown as
dots on the plot (only when pseudo=TRUE).
Colour for pseudo-values.
Dot type (see par) for pseudo-values.
The method for estimating the calibration curve(s):
"nne": The expected event status is obtained in the nearest
neighborhood around the predicted event probabilities.
"quantile": The expected event status is obtained in groups
defined by quantiles of the predicted event probabilities.
If TRUE predicted probabilities are rounded to
two digits before smoothing. This may have a considerable
effect on computing efficiency in large data sets.
The bandwidth for method="nne"
The number of quantiles for method="quantile" and
bars=TRUE.
If TRUE, use barplots to show calibration.
Barplots only. If TRUE, hang bars
corresponding to observed frequencies at the value of the
corresponding prediction.
Barplots only. Names argument passed to
names.arg of barplot.
Barplots only. If TRUE, show
frequencies above the bars.
Gray scale for pseudo-observations.
If FALSE, do not plot the results, just return
a plottable object.
If TRUE the line(s) are added to an existing
plot.
If FALSE no diagonal line is drawn.
Logical. If TRUE draw legend.
If FALSE no axes are drawn.
Limits of x-axis.
Limits of y-axis.
Label for y-axis.
Label for x-axis.
Vector with colors, one for each element of
object. Passed to lines.
Vector with line widths, one for each element of
object. Passed to lines.
lwd Vector with line style, one for each element of
object. Passed to lines.
Passed to lines.
Passed to lines.
For competing risks models, the cause of failure or event of interest
If TRUE axes labels are multiplied by 100 and thus interpretable on a percent scale.
what to do with NA values. Passed to
model.frame
Default cex used for legend and labels.
Used to control the subroutines: plot, axis, lines,
barplot, legend. See SmartControl.
db=sampleData(100,outcome="binary")
fb1=glm(Y~X1+X5+X7,data=db,family="binomial")
fb2=glm(Y~X1+X3+X6+X7,data=db,family="binomial")
xb=Score(list(model1=fb1,model2=fb2),Y~1,data=db,
plots="cal",metrics=NULL)
plotCalibration(xb)
data(Melanoma)
f1 <- CSC(Hist(time,status)~age+sex+epicel+ulcer,data=Melanoma)
f2 <- CSC(Hist(time,status)~age+sex+logthick+epicel+ulcer,data=Melanoma)
x <- Score(list(model1=f1,model2=f2),Hist(time,status)~1,data=Melanoma,
cause= 2,times=5*365.25,plots="cal")
plotCalibration(x)
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