phylocurve.generalized: Align curves of any shape
In phylocurve: Phylogenetic Comparative Methods for High-Dimensional Traits

Description Usage Arguments Value Author(s) References Examples

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

1	phylocurve.generalized(tree, X, Y)

`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

`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

Eric W. Goolsby

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

# 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)