Plot Outliers

Plot Outliers

Usage

# S4 method for class 'OutlierIndex,missing'
plot(
  x,
  ...,
  type = c("dotchart", "distance"),
  robust = TRUE,
  colors = color("discreterainbow"),
  symbols = c(16, 1, 3),
  xlim = NULL,
  ylim = NULL,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topleft")
)

Arguments

x: An OutlierIndex object.
...: Further graphical parameters.
type: A character string specifying the type of plot that should be made. It must be one of "dotchart" or "distance". Any unambiguous substring can be given.
robust: A logical scalar: should robust Mahalanobis distances be displayed? Only used if type is "dotchart".
colors: A vector of colors or a function that when called with a single argument (an integer specifying the number of colors) returns a vector of colors. Will be mapped to the group names.
symbols: A lenth-three vector of symbol specification for non-outliers and outliers (resp.).
xlim: A length-two numeric vector giving the x limits of the plot. The default value, NULL, indicates that the range of the finite values to be plotted should be used.
ylim: A length-two numeric vector giving the y limits of the plot. The default value, NULL, indicates that the range of the finite values to be plotted should be used.
xlab, ylab: A character vector giving the x and y axis labels.
main: A character string giving a main title for the plot.
sub: A character string giving a subtitle for the plot.
ann: A logical scalar: should the default annotation (title and x and y axis labels) appear on the plot?
axes: A logical scalar: should axes be drawn on the plot?
frame.plot: A logical scalar: should a box be drawn around the plot?
panel.first: An an expression to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.
panel.last: An expression to be evaluated after plotting has taken place but before the axes, title and box are added.
legend: A list of additional arguments to be passed to graphics::legend(); names of the list are used as argument names. If NULL, no legend is displayed.

Value

plot() is called for its side-effects: is results in a graphic being displayed (invisibly return x).

References

Filzmoser, P., Garrett, R. G. & Reimann, C. (2005). Multivariate outlier detection in exploration geochemistry. Computers & Geosciences, 31(5), 579-587. doi:10.1016/j.cageo.2004.11.013 .

Filzmoser, P. & Hron, K. (2008). Outlier Detection for Compositional Data Using Robust Methods. Mathematical Geosciences, 40(3), 233-248. doi:10.1007/s11004-007-9141-5 .

Filzmoser, P., Hron, K. & Reimann, C. (2012). Interpretation of multivariate outliers for compositional data. Computers & Geosciences, 39, 77-85. doi:10.1016/j.cageo.2011.06.014 .

Author

N. Frerebeau

Examples

## Data from Day et al. 2011
data("kommos", package = "folio") # Coerce to compositional data
kommos <- remove_NA(kommos, margin = 1) # Remove cases with missing values
coda <- as_composition(kommos, parts = 3:17, groups = 1)

## Detect outliers
out <- detect_outlier(coda)

plot(out, type = "dotchart")

plot(out, type = "distance")


## Detect outliers according to CJ
ref <- extract(coda, "CJ")
out <- detect_outlier(coda, reference = ref, method = "mcd")
plot(out, type = "dotchart")