.prune_tree

Removes species from a phylogenetic tree that are not present in the current data subset
during leave-one-out analysis.

internal

Generates prediction intervals and orchard plots for
meta-analytic and meta-regression models fitted with the 'metafor'
package. Orchard plots augment classic forest plots by displaying
individual effect sizes together with group means and their confidence
and prediction intervals, providing an enhanced visualization of
meta-analytic data for ecology, evolution, and beyond. Methods are
described in Nakagawa et al. (2023) <doi:10.1111/2041-210X.14152>.

Daniel Noble

orchaRd

Visualizing Meta-Analyses with Orchard Plots and Prediction
Intervals

Shinichi Nakagawa

.prune_tree function

<dl><dt>tree</dt>
<dd>A phylogenetic tree object of class "phylo".</dd>
<dt>species_names</dt>
<dd>A vector of species names that should remain in the pruned tree.
These are the species present in the current data subset.</dd></dl>

Arguments

Daniel Noble - daniel.noble@anu.edu.au
Facundo Decunta - fdecunta@agro.uba.ar

Author

Prune Phylogenetic Tree For Leave-One-Out Analysis — .prune_tree

<dl>

<dt>tree</dt>
<dd>A phylogenetic tree object of class "phylo".</dd>


<dt>species_names</dt>
<dd>A vector of species names that should remain in the pruned tree.
These are the species present in the current data subset.</dd>

</dl>

.prune_tree: Prune Phylogenetic Tree For Leave-One-Out Analysis

Description

Usage

Value

Arguments

Author