Description Usage Arguments Value References Examples
This function simulates evolution of a function-valued trait (glm with logit link) under Brownian motion.
1 | sim.curves(nspecies = 30, x_length = 20, startree = FALSE, lambda = 1, seed)
|
nspecies |
Number of species |
x_length |
Number of points on the curve to simulate |
startree |
Simulate using a star tree |
lambda |
Pagel's lambda tree transformation parameter (lambda = 0 for star tree; lambda = 1 for original tree) |
seed |
Optional seed to set for reproducibility |
data |
Data frame with simulated curves formatted appropriately for phylocurve() |
tree |
Phylogenetic tree of class "phylo" |
true_coefs |
True tip and ancestral coefficients for glm logit link |
Pagel, M. 1999. "Inferring the historical patterns of biological evolution". Nature 401:877-884.
1 2 3 4 5 6 7 8 9 10 11 12 | # simulate evolution of a function-valued trait (glm with logit link)
sim_data <- sim.curves()
# perform ancestral curve reconstruction
anc_recon <- phylocurve(y~x,tree = sim_data$tree,data = sim_data$data)
# get tip coefficients and aligned function data
tip.coefficients <- get.tip.coefficients(formula = y~x,tree = sim_data$tree,data = sim_data$data)
data <- get.aligned.function.data(tip.coefficients)
# estimate evolutionary rates
evo.model.fitted <- evo.model(sim_data$tree,data)
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