Character Partitioning


This vignette explains how to conduct automated morphological character partitioning as a pre-processing step for clock (time-calibrated) Bayesian phylogenetic analysis of morphological data, as introduced by Simões and Pierce (2021).

Installing package EvoPhylo

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Character Partitioning

Load the EvoPhylo package


1. Generate distance matrix

Generate a Gower distance matrix with get_gower_dist() by supplying the file path of a .nex file containing a character data matrix:

#Load a character data matrix and produce a Gower distance matrix
dist_matrix <- get_gower_dist("DataMatrix.nex", numeric = FALSE)

Below, we use the example data matrix characters that accompanies EvoPhylo.


dist_matrix <- get_gower_dist(characters, numeric = FALSE)

2. Estimate the optimal number of partitions

The optimal number of partitions (clusters) will be first determined using partitioning around medoids (PAM) with Silhouette widths index (Si) using get_sil_widths(). The latter will estimate the quality of each PAM cluster proposal relative to other potential clusters.

## Estimate and plot number of cluster against silhouette width
sw <- get_sil_widths(dist_matrix, max.k = 10)
plot(sw, color = "blue", size = 1)

Decide on number of clusters based on plot; here, \(k = 3\) partitions appears optimal.

3. Simple Workflow:

3.1. Analyze clusters with PAM under chosen \(k\) value (from Si) with make_clusters().

3.2. Produce simple cluster graph

3.3. Export clusters/partitions to Nexus file with cluster_to_nexus().

## Generate and vizualize clusters with PAM under chosen k value. 
clusters <- make_clusters(dist_matrix, k = 3)


## Write clusters to Nexus file
cluster_to_nexus(clusters, file = "Clusters_Nexus.txt")

4. Complete Workflow:

4.1. Analyze clusters with PAM under chosen \(k\) value (from Si) with make_clusters().

4.2. Produce a graphic clustering (tSNEs), coloring data points according to PAM clusters, to independently verify PAM clustering. This is set with the tsne argument within make_clusters().

4.3. Export clusters/partitions to Nexus file with cluster_to_nexus(). This can be copied and pasted into the Mr. Bayes command block.

#User may also generate clusters with PAM and produce a graphic clustering (tSNEs)
clusters <- make_clusters(dist_matrix, k = 3, tsne = TRUE, tsne_dim = 3)

plot(clusters, nrow = 2, max.overlaps = 5)

#Write clusters/partitions in Nexus file format 
cluster_to_nexus(clusters, file = "Clusters_Nexus.txt")


Simões, Tiago R., and Stephanie E. Pierce. 2021. “Sustained High Rates of Morphological Evolution During the Rise of Tetrapods.” Nature Ecology & Evolution 5 (10): 1403–14.