plot.trajectory.analysis: Plot Function for RRPP

In RRPP: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

Plot Function for RRPP

Description

Function generates a principal component plot for trajectories

Usage

## S3 method for class 'trajectory.analysis'
plot(x, ...)

Arguments

x	plot object (from trajectory.analysis)
...	other arguments passed to plot (helpful to employ different colors or symbols for different groups). See plot.default and par

Details

The function calculates and plots principal components of fitted values from lm.rrpp that are passed onto trajectory.analysis, and projects data onto them. This function is a set.up, and add.trajectories is needed to add trajectories to the plot. By having two stages of control, the plotting functions are more flexible. This function also returns plotting information that can be valuable for making individualized plots, if add.trajectories is not preferred.

Value

If an object is assigned, it will return:

pca	Principal component analysis performed using prcomp.
pc.points	Principal component scores for all data.
trajectory.analysis	Trajectory analysis passed on.
trajectories	pca Observed trajectories projected onto principal components.

Author(s)

Michael Collyer

References

Adams, D. C., and M. M. Cerney. 2007. Quantifying biomechanical motion using Procrustes motion analysis. J. Biomech. 40:437-444.

Adams, D. C., and M. L. Collyer. 2007. The analysis of character divergence along environmental gradients and other covariates. Evolution 61:510-515.

Adams, D. C., and M. L. Collyer. 2009. A general framework for the analysis of phenotypic trajectories in evolutionary studies. Evolution 63:1143-1154.

Collyer, M. L., and D. C. Adams. 2007. Analysis of two-state multivariate phenotypic change in ecological studies. Ecology 88:683-692.

Collyer, M. L., and D. C. Adams. 2013. Phenotypic trajectory analysis: comparison of shape change patterns in evolution and ecology. Hystrix 24: 75-83.

Collyer, M.L., D.J. Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for phenotypes described by high-dimensional data. Heredity. 115:357-365.

See Also

plot.default and par

Examples

# See \code{\link{trajectory.analysis}} for examples

RRPP documentation built on Aug. 16, 2023, 1:06 a.m.