phylocurve (version 2.1.1)

phylocurve.generalized: Align curves of any shape

Description

Aligns curves by x,y coordinates so that species curves can be analyzed as a single high-dimensional trait.

Usage

phylocurve.generalized(tree, X, Y)

Arguments

tree

An object of class phylo

X

A numeric vector of length M, used for each species

Y

An N x M marix where each row corresponds to a species and each column corresponds to index M_i of X

Value

aligned_data

x and y coordinates arranged in a single row vector for each species

aligned_coordinates

x and y coordinates for each species (one data point per row)

aligned_X

Aligned X coordinates in N x M matrix

aligned_Y

Aligned Y coordinates in N x M matrix

nr

Number of aligned landmarks

anc_X

Vector of root X values (assuming Brownian motion)

anc_Y

Vector of root Y values (assuming Brownian motion)

tree

Phylogenetic tree supplied into the function

References

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

Examples

# NOT RUN {
# NOT RUN (takes several minutes)
# x_length <- 50
# nspecies <- 25
#sim_data <- sim.curves(nspecies = nspecies,x_length = x_length)
#
# Perform ancestral curve reconstruction without any assumptions about function shape
# P <- phylocurve.generalized(tree = sim_data$tree,X = sim_data$data$x[1:x_length],
# Y = t(matrix(sim_data$data$y,nrow = x_length,
# dimnames = list(1:x_length,sim_data$tree$tip.label))))
#
# Data might need trimming for values where there is no variation
# plot(P$anc_X,P$anc_Y)
#
# P.trimmed <- phylocurve.trim(phylocurve.generalized = P,min_X = 4,max_X = 8)
# }