est_DAG: Add standardized path coefficients to a DAG.

In phylopath: Perform Phylogenetic Path Analysis

Add standardized path coefficients to a DAG.

Description

Add standardized path coefficients to a DAG.

Usage

est_DAG(DAG, data, tree, model, method, boot = 0, ...)

Arguments

DAG	A directed acyclic graph, typically created with DAG.
data	A data.frame with data. If you have binary variables, make sure they are either character values or factors!
tree	A phylogenetic tree of class phylo.
model	The evolutionary model used for the regressions on continuous variables. See phylolm::phylolm for options and details. Defaults to Pagel's lambda model
method	The estimation method for the binary models. See phylolm::phyloglm for options and details. Defaults to logistic MPLE.
boot	The number of bootstrap replicates used to estimate confidence intervals.
...	Arguments passed on to phylolm: lower.bound: optional lower bound for the optimization of the phylogenetic model parameter. upper.bound: optional upper bound for the optimization of the phylogenetic model parameter. starting.value: optional starting value for the optimization of the phylogenetic model parameter. measurement_error: a logical value indicating whether there is measurement error sigma2_error (see Details). Arguments passed on to phyloglm: btol: bound on the linear predictor to bound the searching space. log.alpha.bound: bound for the log of the parameter alpha. start.beta: starting values for beta coefficients. start.alpha: starting values for alpha (phylogenetic correlation).

Value

An object of class fitted_DAG.

Examples

  d <- DAG(LS ~ BM, NL ~ BM, DD ~ NL + LS)
  plot(d)
  d_fitted <- est_DAG(d, rhino, rhino_tree, 'lambda')
  plot(d_fitted)

phylopath documentation built on June 22, 2024, 10:31 a.m.