MorphSim v1.2.0

First release accompanying the publication:

Mulvey et al. (2026) "MorphSim: An R package for simulating discrete morphological data"

MorphSim is an R package for simulating discrete morphological character data for total-evidence and tip-dated phylogenetic analyses.

Key Features

Evolutionary models

• Mk model and extensions (MkV, ordered variants)
• Among-character rate variation (ACRV) via gamma or lognormal distributions
• User-defined custom rate matrices
• Multi-partition schemes with different states per partition

Fossil & ancestor support

• Simulates character data for sampled ancestors (direct ancestral fossils)
• Integrates with FossilSim, TreeSim, and SimClock for a complete end-to-end pipeline compatible with RevBayes and BEAST2

Realistic missing data

• Structured missing data by anatomical partition with taphonomic decay probabilities
• Missing data by rate category, taxon age, or random removal

Visualisation & summary statistics

• Plot trait evolution history across the full and reconstructed tree
• Consistency and retention indices
• Convergent evolution tracking across all characters

Export

• write.morpho() exports trees, matrices, and fossil ages in formats compatible with RevBayes and BEAST2

MorphSimShiny

An interactive Shiny app for exploring model assumptions and simulating datasets without requiring R expertise. https://github.com/fossilsim/morphsimshiny

Installation

install.packages("MorphSim")

or from GitHub:

devtools::install_github("fossilsim/morphsim")