write_partitioned_alignments: Write character partitions as separate Nexus files (for use...

In EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Write character partitions as separate Nexus files (for use in BEAUti)

Description

Write character partitions as separate Nexus files (for use in BEAUti)

Usage

write_partitioned_alignments(x, cluster_df, file)

Arguments

x	character data matrix as Nexus file (.nex) or data frame (with taxa as rows and characters as columns) read directly from local directory
cluster_df	cluster partitions as outputted by make.clusters
file	path to save the alignments. If file = "example.nex", alignments will be saved to files "example_part1.nex", "example_part2.nex", etc.

Value

no return value

Examples

# Load example phylogenetic data matrix
data("characters")

# Create distance matrix
Dmatrix <- get_gower_dist(characters)

# Find optimal partitioning scheme using PAM under k=3 partitions
cluster_df <- make_clusters(Dmatrix, k = 3)

# Write to Nexus files
## Not run: write_partitioned_alignments(characters, cluster_df, "example.nex")

EvoPhylo documentation built on Nov. 4, 2022, 1:06 a.m.