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., 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 resu..., , # 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 lea...

PCMBase R包（PCMBase R package）是一款功能强大的计算工具，可高效计算多种系统发育高斯模型的似然值。依托该工具，我们对R包mvSLOUCH进行了重新设计。本文演示了如何利用该包的新版本，通过多变量奥恩斯坦-乌伦贝克过程（multivariate Ornstein-Uhlenbeck processes），对包含1252种维管植物的大型数据集开展性状演化与适应的全面分析。本研究的分析结果表明，该建模框架能够有效区分有关被子植物功能性状演化的多种替代假说。

编译完成的维管植物数据集包含两个核心组件：表型数据（plant_data.csv）与系统发育树文件（plant_tree.txt），涵盖以下性状：氮埃伦伯格指示值（记为Nutrients）、叶面积（单位：mm²，记为leaf.area）、株高（单位：m，记为plant.height）、种子质量（单位：mg，记为seed.mass）以及叶质量（单位：mg，记为leaf.mass）。其中，氮埃伦伯格指示值数据引自Chytrý等人（2018）；叶面积、种子质量与叶质量数据引自Carmona等人（2021）；株高数据引自TRY数据库（Kattge等人，2011）。该带时间标定的系统发育树为Carmona等人（2021）所使用的植物超树。

本分析工作在R语言环境中完成，依托华沙大学生物与化学研究中心的FUN–K计算集群，使用单节点48线程完成计算。分析结果的具体数值可能受随机种子影响，但本脚本支持复现论文中的分析流程，即使用生成结果的随机种子……

# 快速mvSLOUCH：基于多变量奥恩斯坦-乌伦贝克过程的大型系统发育性状演化模型
[https://doi.org/10.5061/dryad.8w9ghx3vt](https://doi.org/10.5061/dryad.8w9ghx3vt)

本数据集包含配套论文Bartoszek、Clarke、Fuentes Gonzalez、Mitov、Pienaar、Piwczynski、Puchalka、Spalik与Voje所著《Fast mvSLOUCH: 基于大型系统发育的多变量奥恩斯坦-乌伦贝克性状演化模型》的相关数据、R脚本与数值结果。其中两个数据文件涉及维管植物的功能性状：株高、种子质量、叶面积、叶质量及其氮埃伦伯格指示值，以及对应的系统发育树。

## 数据与文件结构说明
编译完成的维管植物数据集包含两个核心组件：表型数据（plant_data.csv）与系统发育树文件（plant_tree.txt），涵盖以下内容：氮埃伦伯格指示值（记为Nutrients）、叶面积（单位：mm²，记为leaf.area）、株高（单位：m，记为plant.height）、种子质量（单位：mg，记为seed.mass）以及叶质量（原文截断为lea...）。