MRF penalty from a phylogeny from a phylo4 object

MRF penalty from a phylogeny from a phylo4 object

Usage

# S3 method for class 'phylo4'
mrf_penalty(
  object,
  model = c("rw1", "ou", "brownian"),
  alpha = NULL,
  at_tips = NULL,
  internal_nodes = TRUE,
  delta = FALSE,
  ...
)

Arguments

object

an R object to create the MRF penalty from.

model

character; one of "full" or "individual" indicating if a fully connected graph ("full") or a random effect (random intercepts; "individual") penalty is created.

alpha

numeric; the autoregressive parameter for an OU stochastic process. Should be >1e-5 (alpha = 0 would correspond to a "rw1" model).

at_tips

character; vector of tip labels to calculate the penalty at. All values in the vector must correpond to tip name labels in the tree.

internal_nodes

logical; should the internal nodes of the tree be included in the penalty (TRUE), or just the tips (terminal nodes; FALSE)

delta

numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.

...

arguments passed to other methods.

Examples

#loading the geospiza dataset from phylobase
library(phylobase)
data(geospiza)

#Random-walk (rw1) penalty for both tips and nodes:
pen_rw <- mrf_penalty(geospiza, model = "rw1")

#Same model, but for a reduced number of species
species <- c("fortis", "pauper", "fusca", "olivacea")
pen_rw_subset <- mrf_penalty(geospiza, model = "rw1", at_tips = species)
plot(get_obj(pen_rw_subset))


#Random-walk penalty matrix for just the tips for all geospiza data:
pen_rw_tips <- mrf_penalty(geospiza, model = "rw1", internal_nodes = FALSE)
pen_rw_tips
#> Markov Random Field penalty
#> Type: tree
#> N   : 14

#Ornstein-Uhlenbeck ("ou") process penalty matrix, specifying alpha parameter (autocorrelation)
pen_ou <- mrf_penalty(geospiza, model = "ou", alpha = 1)