Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies

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.

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.