Description Usage Arguments Value Author(s) References Examples
Trims curves to specified range of X and Y coordinates
1 2 | phylocurve.trim(phylocurve.generalized, min_Y = -Inf,
max_Y = Inf, min_X = -Inf, max_X = Inf)
|
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 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # 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)
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