phylocurve (version 2.1.1)

phylocurve.trim: Trim aligned curves

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

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)
# }