phylocurve.trim: Trim aligned curves

In ericgoolsby/phylocurve: Phylogenetic Comparative Methods for High-Dimensional Traits

Description

Trims curves to specified range of X and Y coordinates

Usage

phylocurve.trim(phylocurve.generalized, min_Y = -Inf,
  max_Y = Inf, min_X = -Inf, max_X = Inf)

Arguments

phylocurve.generalized	The value returned by the phylocurve.generalized function
min_Y	The minimum Y value for trimming curves
max_Y	The maximum Y value for trimming curves
min_X	The minimum X value for trimming curves
max_X	The maximum X value for trimming curves

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

Author(s)

Eric W. Goolsby

References

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

Examples

# 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)

ericgoolsby/phylocurve documentation built on April 28, 2021, 10:23 p.m.