Data from: Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies
Authors/Creators
- 1. Linköping University
- 2. German Center for Integrative Biodiversity Research
- 3. Florida International University
- 4. IntiQuan GmbH*
- 5. Nicolaus Copernicus University
- 6. University of Warsaw
- 7. University of Oslo
Description
The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models. Taking advantage of it, we redesigned the R package mvSLOUCH. Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein-Uhlenbeck processes. The results of our analysis demonstrate the ability of the modeling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.
Notes
Funding provided by: Swedish Research Council
ROR ID: https://ror.org/03zttf063
Award Number: 2017–04951
Funding provided by: ELLIIT
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100030800
Award Number: Call C
Funding provided by: Foundation for Scientific Research and Education in Mathematics (SVeFUM)*
Crossref Funder Registry ID:
Award Number:
Funding provided by: Alexander von Humboldt Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100005156
Award Number:
Funding provided by: Narodowa Agencja Wymiany Akademickiej
ROR ID: https://ror.org/02jf81j23
Award Number: PPN/ULM/2019/1/00248/U/00001
Funding provided by: Estonian Research Council
ROR ID: https://ror.org/00jjeja18
Award Number: PRG741
Funding provided by: Deutsche Forschungsgemeinschaft
ROR ID: https://ror.org/018mejw64
Award Number: DFG–FZT 118
Funding provided by: National Science Foundation
ROR ID: https://ror.org/021nxhr62
Award Number: 2225683
Funding provided by: National Science Center
ROR ID: https://ror.org/03ha2q922
Award Number: 2015/18/E/NZ8/00716
Funding provided by: European Research Council
ROR ID: https://ror.org/0472cxd90
Award Number: 948465
Funding provided by: Deutsche Forschungsgemeinschaft
ROR ID: https://ror.org/018mejw64
Award Number: 202548816
Methods
The compiled vascular plant dataset involves two key components: phenotypic data (plant_data.csv) and phylogenetic tree (plant_tree.txt), which consist of the following: Ellenberg indicator values for nitrogen (Nutrients), leaf area (leaf.area in mm2), plant height (plant.height in m), seed mass (seed.mass in mg) and leaf mass (leaf.mass in mg).
The Ellenberg indicator values are taken from Chytrý et al. (2018); leaf area, seed mass, and leaf mass are taken from Carmona et al. (2021); and plant height from the TRY database (Kattge et al. 2011). The dated phylogeny is the supertree of plants used by Carmona et al. (2021).
The analyses were completed in R using the computing cluster FUN–K at the Biological and Chemical Research Center, University of Warsaw using one node with 48 threads.
The exact output can depend on the random seed. However, in the script we have the option of rerunning the analyses as it was in the manuscript, i.e.
the random seeds that were used to generate the results are saved, included and can be read in.
The code is divided into several directories with scripts, random seeds and result files.
1) PhasePlanesmvOU
R code to generate Figures 1 and S1 of the manuscript.
2) PlantFunctionalTraits
This directory contains files connected to the analyses of vascular plants performed for the manuscript. The main directory contains all the R scripts required to replicate the analyses (or run a new version). The Data directory contains the data for analyses, RandomSeeds the random seeds, InvidRuns the results of individual runs (starting points for the numerical optimization) of the estimation procedure, and Results the results of all of the analyses.
3) RegimeMapping
Code that illustrates how to use the output of stochastic character mapping for providing mvSLOUCH with a regime layout. This is code accompanies "Appendix SC7: Importing stochastic character mapping to mvSLOUCH: example analysis" from the Supplementary Material to the manuscript.
4) Timings
A simulation study to compare the running times between the old (1.3.4) and new (2.7.3) versions of mvSLOUCH. Done in R version 3.6.1 (2019-09-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: openSUSE Leap 42.3
C. P. Carmona, R. Tamme M. Pärtel, F. de Bello, S. Brosse, P. Capdevila, R. M. González, M. González–Suárez, R. Salguero–Gómez, M. Vásquez–Valderrama, and A. Toussaint. Erosion of global functional diversity across the tree of life. Sci. Adv., 7, 2021.
M. Chytrý, L. Tichý, P. Dřevojan, J. Sádlo, and D. Zelený. Ellenberg–type indicator values for the Czech flora. Preslia, 90:83–103, 2018.
J. Kattge et. al. TRY-a global database of plant traits. Glob. Chang. Biol., 17:2905–2935, 2011.
Files
plant_data.csv
Additional details
Related works
- Is derived from
- 10.5281/zenodo.11286569 (DOI)