# calibration

##### Probability Calibration Plot

For classification models, this function creates a 'calibration plot' that describes how consistent model probabilities are with observed event rates.

- Keywords
- hplot

##### Usage

`calibration(x, ...)`## S3 method for class 'formula':
calibration(x, data = NULL,
class = NULL,
cuts = 11, subset = TRUE,
lattice.options = NULL, ...)

## S3 method for class 'calibration':
xyplot(x, data, ...)

panel.calibration(...)

##### Arguments

- x
- a
`lattice`

formula (see`xyplot`

for syntax) where the left-hand side of the formula is a factor class variable of the observed outcome and the right-hand side specifies one or model - data
- For
`calibration.formula`

, a data frame (or more precisely, anything that is a valid`envir`

argument in`eval`

, e.g., a list or an environment) containing values for any variables in the formula, as well as`groups`

- class
- a character string for the class of interest
- cuts
- the number of splits of the data are used to create the plot. By default, it uses as many cuts as there are rows in
`data`

- subset
- An expression that evaluates to a logical or integer indexing vector. It is evaluated in
`data`

. Only the resulting rows of`data`

are used for the plot. - lattice.options
- A list that could be supplied to
`lattice.options`

- ...
- options to pass through to
`xyplot`

or the panel function (not used in`calibration.formula`

).

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##### Details

`calibration.formula`

is used to process the data and `xyplot.calibration`

is used to create the plot.

To construct the calibration plot, the following steps are used for each model:

- The data are split into
`cuts - 1`

roughly equal groups by their class probabilities - the number of samples with true results equal to
`class`

are determined - the event rate is determined for each bin

`xyplot.calibration`

produces a plot of the observed event rate by the mid-point of the bins. This implementation uses the lattice function `xyplot`

, so plot elements can be changed via panel functions, `trellis.par.set`

or other means. `calibration`

uses the panel function `panel.calibration`

by default, but it can be changed by passing that argument into `xyplot.calibration`

.

The folowing elements are set by default in the plot but can be changed by passing new values into `xyplot.calibration`

: `xlab = "Bin Midpoint"`

, `ylab = "Observed Event Percentage"`

, `type = "o"`

, `ylim = extendrange(c(0, 100))`

,`xlim = extendrange(c(0, 100))`

and `panel = panel.calibration`

##### Value

`calibration.formula`

returns a list with elements:data the data used for plotting cuts the number of cuts class the event class probNames the names of the model probabilities `xyplot.calibration`

returns a lattice object

##### See Also

##### Examples

```
data(mdrr)
mdrrDescr <- mdrrDescr[, -nearZeroVar(mdrrDescr)]
mdrrDescr <- mdrrDescr[, -findCorrelation(cor(mdrrDescr), .5)]
inTrain <- createDataPartition(mdrrClass)
trainX <- mdrrDescr[inTrain[[1]], ]
trainY <- mdrrClass[inTrain[[1]]]
testX <- mdrrDescr[-inTrain[[1]], ]
testY <- mdrrClass[-inTrain[[1]]]
library(MASS)
ldaFit <- lda(trainX, trainY)
qdaFit <- qda(trainX, trainY)
testProbs <- data.frame(obs = testY,
lda = predict(ldaFit, testX)$posterior[,1],
qda = predict(qdaFit, testX)$posterior[,1])
calibration(obs ~ lda + qda, data = testProbs)
calPlotData <- calibration(obs ~ lda + qda, data = testProbs)
calPlotData
xyplot(calPlotData, auto.key = list(columns = 2))
```

* Documentation reproduced from package caret, version 6.0-24,
License: GPL-2
*
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