DOI: 10.5061/dryad.8w9ghx3vt
title: Data from: Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies

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.
description: 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 mm<sup>2</sup>), plant
 height (plant.height in m), seed mass (seed.mass in mg) and leaf mass
 (leaf.mass in mg).<br>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). <br>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.<br>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<br>R code to
 generate Figures 1 and S1 of the manuscript. 2)
 PlantFunctionalTraits<br>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<br>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<br>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.<br>M. Chytrý, L. Tichý, P. Dřevojan, J. Sádlo, and D. Zelený.
 Ellenberg–type indicator values for the Czech flora. Preslia, 90:83–103,
 2018.<br>J. Kattge et. al. TRY-a global database of plant traits.
 Glob. Chang. Biol., 17:2905–2935, 2011.
description: # Fast mvSLOUCH: multivariate Ornstein-Uhlenbeck-based models of trait
 evolution on large phylogenies
 [https://doi.org/10.5061/dryad.8w9ghx3vt](https://doi.org/10.5061/dryad.8w9ghx3vt) These are the data, R scripts and numerical results accompanying Bartoszek, Clarke, Fuentes Gonzalez, Mitov, Pienaar, Piwczynski, Puchalka, Spalik and Voje " Fast mvSLOUCH: multivariate Ornstein–Uhlenbeck-based models of trait evolution on large phylogenies". The two data files concern functional traits in vascular plants: plant height, seed mass, leaf area, leaf mass and their Ellenberg indicator values for nitrogen, and their phylogeny. ## Description of the data and file structure 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. ## Sharing/Access information Data was derived from the following sources: * 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. ## Code/Software 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