Phylogenetic comparative methods (PCMs) can be used to study evolutionary relationships and trade-offs among species traits. Analysts using PCM may want to (1) include latent variables, (2) estimate complex trait interdependencies, (3) predict missing trait values, (4) condition predicted traits upon phylogenetic correlations and (5) estimate relationships as slope parameters that can be compared with alternative regression methods. The Comprehensive R Archive Network (CRAN) includes well-documented software for phylogenetic linear models (phylolm), phylogenetic path analysis (phylopath), phylogenetic trait imputation (Rphylopars) and structural equation models (sem), but none of these can simultaneously accomplish all five analytical goals. We therefore introduce a new package phylosem for phylogenetic structural equation models (PSEM) and summarize features and interface. We also describe new analytical options, where users can specify any combination of Ornstein-Uhlenbeck, Pagel's-δ and Pagel's-λ transformations for species covariance. For the first time, we show that PSEM exactly reproduces estimates (and standard errors) for simplified cases that are feasible in sem, phylopath, phylolm and Rphylopars and demonstrate the approach by replicating a well-known case study involving trade-offs in plant energy budgets.

中文翻译：

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phylosem：一个快速、简单的 R 包，用于使用系统发育结构方程模型进行系统发育推断和性状插补。

系统发育比较方法（PCM）可用于研究物种性状之间的进化关系和权衡。使用 PCM 的分析师可能希望 (1) 包括潜在变量，(2) 估计复杂的性状相互依赖性，(3) 预测缺失的性状值，(4) 根据系统发育相关性条件预测性状，以及 (5) 将关系估计为斜率参数，这些斜率参数可以是与其他回归方法相比。综合 R 档案网络 (CRAN) 包括用于系统发育线性模型 (phylolm)、系统发育路径分析 (phylopath)、系统发育性状插补 (Rphylopars) 和结构方程模型 (sem) 的记录齐全的软件，但这些软件都无法同时完成所有任务五个分析目标。因此，我们为系统发育结构方程模型（PSEM）引入了一个新的包phylosem，并总结了功能和接口。我们还描述了新的分析选项，用户可以为物种协方差指定 Ornstein-Uhlenbeck、Pagel's-δ 和 Pagel's-λ 变换的任意组合。我们首次证明 PSEM 准确再现了在 sem、phylopath、phylolm 和 Rphylopars 中可行的简化情况的估计（和标准误差），并通过复制涉及植物能量权衡的著名案例研究来演示该方法预算。