paleoTS_test

Examine paleoTS model selection performance with time series length

Introduction

Hohmann et al 2023 (DOI: 10.1101/2023.12.18.572098), supplementary code (DOI: 10.5281/zenodo.10390267) found unexpected behavior in the model selection performance of the paleoTS package, version 0.5.3 (CRAN.R-project.org/package=paleoTS) when including Ornstein-Uhlenbeck processes in the set of modes of evolution tested for. Here, this behavior is examined using the simulation tools implemented in the paleoTS package.

The code simulates stasis and undirected random walks, and examines how AICc weights for different modes of evolution (stasis, (un)directed random walk) change with time series length.

Authors

Niklas Hohmann (maintainer)
Utrecht University
email: n.h.hohmann [at] uu.nl
Web page: www.uu.nl/staff/NHohmann
ORCID: 0000-0003-1559-1838

Melanie Hopkins
American Museum of Natural History
Web page: www.amnh.org/research/staff-directory/melanie-j-hopkins
ORCID: 0000-0002-3580-2172

Melanie Hopkins provided the original code, which was modified by Niklas Hohmann. For detailed author contributions please inspect the git history.

Requirements

R (version >= 4) and the RStudio IDE

Usage

In RStudio, open the file paleoTS_test.Rproj. This will open the RProject of the same name, and install the renvpackage (if not already installed). Then, execute

renv::restore()

in RStudios console to install all required dependencies, including paleoTS version 0.5.3. Now the environment is set up, and you can run the analysis using

source("code/test.paleots.R")

Results of the analysis are already stored in the repository under figs/. You can inspect the code in the file code/test.paleots.R.

License

Apache 2.0, see LICENSE file for full license text.

Repository structure

• code : folder for code
  • test.paleots.R : R script examining paleoTS model selection with time series length
• figs : folder for figures
  • test_stasis_with_ou.jpeg : AICc weights under stasis model with increasing time series length, including OU in the tested modes
  • test_stasis_without_ou.jpeg : AICc weights under stasis model with increasing time series length, not including OU in the tested modes
  • test_urw_with_ou.jpeg : AICc weights under undirected random walk (URW) model with increasing time series length, including OU in the tested modes
  • test_urw_without_ou.jpeg : AICc weights under undirected random walk (URW) model with increasing time series length, not including OU in the tested modes
• renv : folder for renv package
• .Rprofile : R session info
• .gitignore : untracked files
• LICENSE : Apache 2.0 license text
• README.md : readme file
• paleoTS_test.Rproj : RProject file
• renv.lock : lock file for renv package

Citation

Please use the doi given at the beginning of this document to cite this repository.

Funding information

Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.