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lefko3: Analysing individual history through size‐classified matrix population models
Methods in Ecology and Evolution ( IF 6.3 ) Pub Date : 2020-11-15 , DOI: 10.1111/2041-210x.13526
Richard P. Shefferson 1 , Shun Kurokawa 1 , Johan Ehrlén 2
Affiliation  

  1. The histories of individuals impact the dynamics of their populations. Matrix projection models (MPMs) are used to analyse population dynamics, but are not structured to incorporate these influences. Historical MPMs (hMPM) were developed to incorporate these impacts, but their complexity has left them little used. We developed r package lefko3 to provide simple, quick methods to estimate and analyse hMPMs, as well as ahistorical MPMs.
  2. Package lefko3 handles the entire workflow from dataset organization to the construction and analysis of hMPMs. Dataset management functions reorganize most demographic data formats, and matrix creation functions estimate both raw and function‐based matrices. Vital rates may be modelled as mixed or generalized linear models, with model selection protocols involving current best practices.
  3. The core kernels are binaries allowing even matrices with over 10,000 rows and columns to be estimated quickly without parallelization. We also include functions to conduct basic deterministic projection analyses.
  4. Package lefko3, available on CRAN, dramatically reduces the difficulties in testing the impacts of individual history on population dynamics. We provide three vignettes to showcase how hMPMs can be developed and analysed.


中文翻译:

lefko3:通过按大小分类的矩阵人口模型分析个人历史

  1. 个人的历史会影响其人口动态。矩阵投影模型(MPM)用于分析人口动态,但其结构并未纳入这些影响。历史MPM(hMPM)旨在合并这些影响,但是它们的复杂性使其很少使用。我们开发[Rlefko3提供简单,快捷的方法来估计和分析hMPMs,以及与历史无关的MPM。
  2. 软件包lefko3处理从数据集组织到hMPM的构建和分析的整个工作流程。数据集管理功能可重组大多数人口统计数据格式,矩阵创建功能可估算原始矩阵和基于函数的矩阵。可以将活率建模为混合或广义线性模型,模型选择协议涉及当前的最佳实践。
  3. 核心内核是二进制文件,即使不具有并行性,也可以快速估计甚至具有10,000行和以上列的矩阵。我们还包括进行基本确定性投影分析的功能。
  4. CRAN上可用的软件包lefko3大大减少了测试个人历史对人口动态影响的难度。我们提供了三个短片来展示如何开发和分析hMPM。
更新日期:2020-11-15
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