1. Model‐based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model‐based methods do not include phylogenies despite the well‐known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily.
2. To fill this gap, the r package phyr (pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. The phyr workhorse functions are implemented in C++ making all calculations and model estimations fast.
3. phyr can fit a variety of models such as phylogenetic joint‐species distribution models, spatiotemporal‐phylogenetic autocorrelation models, and phylogenetic trait‐based bipartite network models. phyr also estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. All phyr methods are united under Brownian motion or Ornstein–Uhlenbeck models of evolution, and phylogenetic terms are modelled as phylogenetic covariance matrices.
4. The functions and model formula syntax we propose in phyr provide an easy‐to‐use collection of tools that we hope will ignite the use of phylogenies to address a variety of ecological questions.

中文翻译：

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phyr：生态群落系统发育物种分布模型的r包

1. 基于模型的方法在生态学研究中越来越受欢迎。这种趋势的一个很好的例子是使用联合物种分布模型来询问有关生态群落的问题。然而，尽管众所周知，系统发育关系在塑造物种分布和群落组成中非常重要，但目前大多数基于模型方法的应用都不包括系统发育。部分原因是由于缺少可访问的工具，这些工具无法使生态学家轻松拟合系统发育物种分布模型。
2. 为了填补这一空白，R软件包phyr（发音为fire）实施了一套度量，比较方法和混合模型，这些系统使用系统发育来理解和预测群落组成以及其他生态和进化现象。该的PhyR主力功能是用C ++实现让所有的计算和模型估计快。
3. phyr可以适合多种模型，例如系统发育联合物种分布模型，时空系统发育自相关模型以及基于系统发育特征的双向网络模型。phyr还估计具有系统误差的系统发生独立性状相关性，以测试适应性综合症，并快速计算常见的α和β系统发生多样性指标。所有phyr方法都在布朗运动或Ornstein-Uhlenbeck进化模型下结合在一起，并且系统发育术语被建模为系统进化协方差矩阵。
4. 我们在phyr中提出的功能和模型公式语法提供了易于使用的工具集合，我们希望这些工具能够激发系统发育的使用来解决各种生态问题。