coef_plot: Plot path coefficients and their confidence intervals or...

In phylopath: Perform Phylogenetic Path Analysis

Plot path coefficients and their confidence intervals or standard errors.

Description

Plot path coefficients and their confidence intervals or standard errors.

Usage

coef_plot(
  fitted_DAG,
  error_bar = "ci",
  order_by = "default",
  from = NULL,
  to = NULL,
  reverse_order = FALSE
)

Arguments

fitted_DAG	A fitted DAG, usually obtained by best(), average() or est_DAG().
error_bar	Whether to use confidence intervals ("ci") or standard errors ("se") as error bars. Will force standard errors with a message if confidence intervals are not available.
order_by	By "default", the paths are ordered as in the the model that is supplied. Usually this is in the order that was established by ⁠[phylo_path()]⁠ for all combined graphs. This can be change to "causal" to do a reordering based on the model at hand, or to "strength" to order them by the standardized regression coefficient.
from	Only show path coefficients from these nodes. Supply as a character vector.
to	Only show path coefficients to these nodes. Supply as a character vector.
reverse_order	If TRUE, the paths are plotted in reverse order. Particularly useful in combination with ggplot2::coord_flip() to create horizontal versions of the plot.

Value

A ggplot object.

Examples

  d <- DAG(LS ~ BM, NL ~ BM, DD ~ NL + LS)
  plot(d)
  d_fitted <- est_DAG(d, rhino, rhino_tree, 'lambda')
  plot(d_fitted)
  coef_plot(d_fitted, error_bar = "se")
  # to create a horizontal version, use this:
  coef_plot(d_fitted, error_bar = "se", reverse_order = TRUE) + ggplot2::coord_flip()

phylopath documentation built on Oct. 10, 2023, 1:05 a.m.