R: Plot Mahalanobis distance for a fitted smn.lmm or smsn.lmm

plot.mahalDist

R Documentation

Plot Mahalanobis distance for a fitted smn.lmm or smsn.lmm

Description

Plot method for objects of class "mahalDist". For the total Mahalanobis distance, it gives a quantile for outlier detection, based on the Mahalanobis distance theoretical distribution.

Usage

## S3 method for class 'mahalDist'
plot(x, fitobject, type, level = 0.99, nlabels = 3, ...)

Arguments

`x`	An object inheriting from class `mahalDist`, representing the Mahalanobis distance from a fitted scale mixture of (skew) normal linear mixed model.
`fitobject`	Optional. An object inheriting from class `SMN` or `SMSN`, representing the fitted scale mixture of (skew) normal linear mixed model that was used for calculating the Mahalanobis distance.
`type`	Optional. Either `"total"` (default), for the standard Mahalanobis distance, `"error"`, for the error term of the decomposition, or `"b"` for the random effect term of the decomposition. For details see `mahalDist`.
`level`	An optional numeric value in (0,1) indicating the level of the quantile. It only has utility if `type="total"`. Default is `0.99`.
`nlabels`	Number of observations that should be labeled. Default is 3.
`...`	Additional arguments.

Value

A ggplot object, plotting the index versus the Mahalanobis distance, if all subject have the same number of observations; or plotting the number of observations per subject versus the Mahalanobis, otherwise.

Author(s)

Fernanda L. Schumacher, Larissa A. Matos and Victor H. Lachos

Examples

fm1 = smn.lmm(distance ~ age+Sex, data=nlme::Orthodont, groupVar="Subject")
plot(mahalDist(fm1), nlabels=2)

#the estimated quantile is stored at the attribute "info" of the plot object
plotMD = plot(mahalDist(fm1))
attr(plotMD, "info")