est_DAG: Add standardized path coefficients to a DAG.

Description Usage Arguments Value Examples

View source: R/DAG.R

Description

Add standardized path coefficients to a DAG.

Usage

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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

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

Example output



phylopath documentation built on Oct. 5, 2021, 1:06 a.m.