bre: Specify a branch length (random) effect

In rdinnager/fibre: Fast Evolutionary Trait Modelling on Phylogenies using Branch Regression Models

Specify a branch length (random) effect

Description

This function is meant to be called only in the formula argument of fibre().

Usage

bre(
  phyf,
  rate_distribution = c("iid", "laplacian", "student-t", "horseshoe", "Brownian", "re"),
  hyper = list(prec = list(prior = "pc.prec", param = c(1, 0.1))),
  latent = 0,
  label = NULL,
  standardise = TRUE
)

Arguments

phyf	A pfc column containing the phylogenetic structure
rate_distribution	What distribution to use to model rates of evolution?
hyper	Hyper parameters as a list. Specify the prior distribution for engine = INLA models here. Default is a penalised complexity prior with 10% prior probability density greater than 1, which tend to work well for standardised Gaussian responses and Binomial responses.
latent	How many latent variables to generate in engine = INLA models. Default is none.
label	An optional label used to identify the random effect later The default is a label generated from the expression in phyf
standardise	Should the pfc object be standardised based on it's implied typical variance for terminal nodes? Default: TRUE. This helps random effects to be comparable to each other.

Value

A list of data to be used by the model.

rdinnager/fibre documentation built on Dec. 14, 2024, 10:33 a.m.