# plotAddEllipses: Add Prediction Ellipses to a Plot In MorphoTools2: Multivariate Morphometric Analysis

## Description

This function draws prediction ellipses around taxa.

## Usage

 1 2 plotAddEllipses(result, axes = c(1,2), probability = 0.95, col = "black", type = "l", lty = 1, lwd = 1, ...) 

## Arguments

 result result of pca.calc, pcoa.calc, nmds.calc, or cda.calc, has to by plotted at first. axes x, y axes of plot. probability probability, that a new independent observation from the same population will fall in that ellipse. col the colours for labels. type character indicating the type of plotting, for details, see plot: "p" for points, "l" for lines, "b" for both points and lines, "c" for empty points joined by lines, "o" for overplotted points and lines, "s" and "S" for stair steps and "h" for histogram-like vertical lines. lty the line type. Line types can either be specified as one of following types: 0=blank, 1=solid (default), 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash. lwd the line width. ... further arguments to be passed to lines or other graphical parameters in par.

## Details

Prediction ellipses with given probability define the regions where will fall any new independent observation from the respective taxa. The prediction ellipses are quantified using covariance matrices of taxa scores and chi-squared distribution with two degrees of freedom (Friendly et al. 2013).

## Value

None. Used for its side effect of adding elements to a plot.

## References

Friendly M., Monette G., Fox J. (2013). Elliptical insights: understanding statistical methods through elliptical geometry. Statistical Science 28, 1-39.

## Examples

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 data(centaurea) centaurea = naMeanSubst(centaurea) centaurea = deletePopulation(centaurea, populationName = c("LIP", "PREL")) pcaRes = pca.calc(centaurea) plotPoints(pcaRes, col = c(rgb(255, 0, 0, max = 255, alpha = 150), # red rgb(0, 255, 0, max = 255, alpha = 150), # green rgb(0, 0, 255, max = 255, alpha = 150), # blue rgb(0, 0, 0, max = 255, alpha = 150)), # black legend = FALSE, xlim = c(-5, 7.5), ylim = c(-5, 5.5)) plotAddLegend(pcaRes, col = c("red", "green", "blue", "black"), ncol = 2) plotAddEllipses(pcaRes, col = c("red", "green", "blue", "black"), lwd = 3) 

MorphoTools2 documentation built on Dec. 11, 2021, 9:55 a.m.