Phylogenetic Comparative Methods for Function-Valued and Other High-Dimensional Traits

Share:

Description

Tools for studying the evolution of high-dimensional traits (in particular, function-valued traits), including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution.

Details

Package: phylocurve
Type: Package
Version: 2.0.7
Date: 2016-12-01
License: GPL (>= 2)

Author(s)

Eric W. Goolsby <eric.goolsby.evolution@gmail.com>

References

Goolsby, E.W. 2015. "Phylogenetic comparative methods for evaluating the evolutionary history of function-valued traits." Systematic Biology. In press.

Adams, D.C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution. 68:2675-2688.

Adams, D.C. 2014. A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data. Systematic Biology. 63:685-697.

Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
require(phytools)

# simulate evolution of a function-valued trait (glm with logit link)
sim_data <- sim.curves()

# perform ancestral curve reconstruction
anc_recon <- phylocurve(y~x,tree = sim_data$tree,data = sim_data$data)

# get tip coefficients and aligned function data
tip_coefficients <- get.tip.coefficients(formula = y~x,tree = sim_data$tree,data = sim_data$data)
data <- get.aligned.function.data(tip_coefficients)

# estimate evolutionary rates
evo.model.fitted <- evo.model(sim_data$tree,data)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.