h_process_recon: Prepare HiSSE marginal reconstruction for plotting

In teofiln/utilhisse: A Collection of Functions for Summarising and Visualizing 'hisse' Results

Description

A function to process the output from hisse::MarginRecon. First we get model averaged rates for tips and nodes of the phylogeny. Then convert the tree from phylo format into a treedata class and assign the data.frame of mode-averaged rates to the @data slot. We output the node and tip rates tables and the reformated tree object for downstream plotting with ggtree and ggplot.

Usage

h_process_recon(hisse_recon)

Arguments

hisse_recon

An object produced by hisse::MarginRecon, or a list of such objects over which we can model-average using hisse::GetModelAveRates

Value

A list with three components:

• tree_data the phylogeny with associated data object with reconstructed ancestral, model-averaged node and tip states and rates

• tip_rates/node_rates a tibble of reconstructed ancestral, model-averaged tip/node states and rates.

Examples

data("diatoms")
processed_hisse <- h_process_recon(hisse_recon=diatoms$cid4_recon)
processed_hisse$tip_rates
processed_hisse$node_rates
processed_hisse$tree_data

teofiln/utilhisse documentation built on Sept. 3, 2020, 2:55 p.m.