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ipmr: Flexible implementation of Integral Projection Models in R
Methods in Ecology and Evolution ( IF 6.6 ) Pub Date : 2021-07-22 , DOI: 10.1111/2041-210x.13683
Sam C. Levin 1, 2, 3 , Dylan Z. Childs 4 , Aldo Compagnoni 1, 2, 3 , Sanne Evers 1, 2, 5 , Tiffany M. Knight 1, 2, 5 , Roberto Salguero‐Gómez 3
Affiliation  

  1. Integral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits (e.g. size, height, body mass). Researchers use IPMs to investigate questions ranging from linking drivers to population dynamics, planning conservation and management strategies, and quantifying selective pressures in natural populations. The popularity of stage-structured population models has been supported by R scripts and packages (e.g. IPMpack, popbio, popdemo, lefko3) aimed at ecologists, which have introduced a broad repertoire of functionality and outputs. However, pressing ecological, evolutionary and conservation biology topics require developing more complex IPMs, and considerably more expertise to implement them. Here, we introduce ipmr, a flexible R package for building, analysing and interpreting IPMs.
  2. The ipmr framework relies on the mathematical notation of the models to express them in code format. Additionally, this package decouples the model parameterization step from the model implementation step. The latter point substantially increases ipmr's flexibility to model complex life cycles and demographic processes.
  3. ipmr can handle a wide variety of models, including those that incorporate density dependence, discretely and continuously varying stochastic environments, and multiple continuous and/or discrete traits. ipmr can accommodate models with individuals cross-classified by age and size. Furthermore, the package provides methods for demographic analyses (e.g. asymptotic and stochastic growth rates) and visualization (e.g. kernel plotting).
  4. ipmr is a flexible R package for integral projection models. The package substantially reduces the amount of time required to implement general IPMs. We also provide extensive documentation with six vignettes and help files, accessible from an R session and online.


中文翻译:

ipmr:在 R 中灵活实现积分投影模型

  1. 积分投影模型 (IPM) 是研究由一个或多个连续特征(例如大小、身高、体重)构成的种群动态的重要工具。研究人员使用 IPM 来调查从将驱动因素与种群动态联系起来、规划保护和管理策略以及量化自然种群的选择压力等问题。阶段结构种群模型的普及已经由支持[R脚本和安装包(如IPMpackpopbiopopdemolefko3) 针对生态学家,他们引入了广泛的功能和输出。然而,紧迫的生态、进化和保护生物学主题需要开发更复杂的 IPM,并需要更多的专业知识来实施它们。在这里,我们介绍了ipmr,这是一个用于构建、分析和解释 IPM的灵活R包。
  2. ipmr框架依赖于模型的数学符号来表达他们的代码格式。此外,该包将模型参数化步骤与模型实现步骤分离。后一点大大增加了ipmr对复杂生命周期和人口过程建模的灵活性。
  3. ipmr可以处理各种各样的模型,包括那些包含密度依赖性、离散和连续变化的随机环境以及多个连续和/或离散特征的模型。ipmr可以容纳按年龄和大小交叉分类的个人模型。此外,该软件包还提供了用于人口统计分析(例如渐近和随机增长率)和可视化(例如内核绘图)的方法。
  4. ipmr是用于积分投影模型的灵活R包。该软件包大大减少了实施通用 IPM 所需的时间。我们还提供了包含六个小插图和帮助文件的大量文档,可从 R 会话和在线访问。
更新日期:2021-07-22
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