R: mclust Analysis in 3D

mclust3D {ChemoSpec} | R Documentation

## mclust Analysis in 3D

### Description

This function conducts an mclust analysis of the data provided, and plots the points in 3D using rgl graphics. An option is provided for displaying either classical or robust confidence ellipses. An internal function not generally called by the user. See `mclust3dSpectra` instead.

### Usage

    mclust3D(data, ellipse = TRUE, rob = FALSE, cl = 0.95,
      frac.pts.used = 0.8, truth = NULL, title = "no title provided",
      t.pos = NULL, lab.opts = FALSE, use.sym = FALSE, ...)

### Arguments

`data` | A matrix of 3 columns (corresponding to x, y, z) and samples in rows.
`ellipse` | Logical indicating if confidence ellipses should be drawn.
`rob` | Logical; if `ellipse = TRUE`, indicates that robust confidence ellipses should be drawn. If `FALSE`, classical confidence ellipses are drawn.
`cl` | A number indicating the confidence interval for the ellipse.
`frac.pts.used` | If `ellipse = TRUE` and `rob = TRUE`, a number indicating the fraction of the data points to be considered "good" and thus used to compute the robust confidence ellipse.
`truth` | A character vector indicating the known group membership for reach row of the PC scores. Generally this would be `spectra$groups`.
`title` | A character string for the plot title.
`t.pos` | A character selection from `LETTERS[1:8]` ( = A through H) indicating the desired location for the title.
`lab.opts` | A logical indicating whether or not to display the locations where the title and legend can be placed. These locations are the corners of a cube surrounding the data.
`use.sym` | logical; if true, the color scheme is changed to black and symbols are used for plotting.
`...` | Other parameters to be passed downstream.

### Value

The mclust model is returned invisibly, and a plot is produced.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

`Mclust` for background on the method.

### Examples

    ## Not run:

    require("mclust")
    set.seed(666)
    x <- c(rnorm(10, 3, 0.5), rnorm(10, -1, 0.5))
    y <- c(rnorm(10, 1, 1), rnorm(10, -4, 0.5))
    z <- c(rnorm(10, -2, 0.5), rnorm(10, 3, 0.5))
    x[15] <- y[15] <- z[15] <- 4 # screw up one point
    my.truth <- c(rep("Z", 10), rep("Q", 10))
    mclust3D(cbind(x, y, z), title = "mclust3D demo",
    	 t.pos = "G", truth = my.truth)

    ## End(Not run)

[Package ChemoSpec version 4.4.97 Index]