Package: MorphSim 1.2.0

MorphSim: Simulate Discrete Character Data along Phylogenetic Trees

Tools to simulate morphological traits along phylogenetic trees with branch lengths representing evolutionary distance or time. Includes functions for visualizing evolutionary processes along trees and within morphological character matrices.

Authors:Laura Mulvey [aut, cre, cph], Tim Brandler [aut, cph], Alessio Capobianco [aut, cph], Rachel Warnock [aut, cph], Joelle Barido-Sottani [aut, cph]

MorphSim_1.2.0.tar.gz
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MorphSim_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MorphSim/json (API)

# Install 'MorphSim' in R:

install.packages('MorphSim', repos = c('https://laumul.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

morpho_data - Example morpho dataset

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.00 score 3 scripts 214 downloads 21 exports 36 dependencies

Last updated from:b0a9a99dac. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	163
source / vignettes	OK	288
linux-release-x86_64	OK	161
macos-release-arm64	OK	187
macos-oldrel-arm64	OK	181
windows-devel	OK	105
windows-release	OK	161
windows-oldrel	OK	101
wasm-release	OK	121

Exports:as.morpho combine.morpho convergent_evol get_gamma_rates get_lognormal_rates get.convergent get.matrix get.reconstructed get.transitions is.morpho morpho plotMorphoGrid sim.missing.data sim.morpho stats.morpho symmetric.Q.matrix write.morpho write.recon.matrix write.recon.tree write.recon.tsv write.tsv

Dependencies:ape cli cpp11 digest dplyr fastmatch FossilSim fs generics glue igraph lattice lazyeval lifecycle magrittr Matrix nlme phangorn pillar pkgconfig purrr quadprog R6 rappdirs Rcpp rlang stringi stringr tibble tidyr tidyselect tidytree utf8 vctrs withr yulab.utils

Introduction to MorphSim

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-05-06
Started: 2026-05-06

Help page	Topics
Combine Two Morpho Objects	combine.morpho
Determines the number of convergently evolved traits	convergent_evol
Determines the route (nodes and branches) for a tip in a phylogenetic tree	find_path_to_tip
Get discrete gamma rates	get_gamma_rates
Get discrete log-normal rates	get_lognormal_rates
Identify convergent traits	get.convergent
Get Specific Morphological Matrix	get.matrix
Add reconstructed tree and matrix to morpho object	get.reconstructed
Get Tranisition History	get.transitions
Morpho object	as.morpho is.morpho morpho
Example morpho dataset	morpho_data
Match sampled ancestor labels	morphsim_fossilsim
Plot full evolutionary history	plot.morpho
Plots morphological matrix	plotMorphoGrid
Get reconstructed matrix	reconstruct.matrix
Color branches for plotting a reconstructed tree	reconstruct.tree
Remove morphological character data	sim.missing.data
Simulate characters along branches in a tree	sim.morpho
Calculates statistics for a morpho object	stats.morpho
Generate a symmetric Q matrix	symmetric.Q.matrix
Write morpho data to file	write.morpho
Write reconstructed character matrix to file	write.recon.matrix
Write reconstructed tree to file	write.recon.tree
Write the taxa ages of reconstructed tree	write.recon.tsv
Write the taxa ages	write.tsv

Package: MorphSim 1.2.0

MorphSim: Simulate Discrete Character Data along Phylogenetic Trees

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)