Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK.
Wildfowl and Wetlands Trust, Slimbridge, Gloucester, UK.
J Anim Ecol. 2024 Jul;93(7):784-795. doi: 10.1111/1365-2656.14111. Epub 2024 Jun 11.
Ongoing technological advances have led to a rapid increase in the number, type and scope of animal-tracking studies. In response, many software tools have been developed to analyse animal movement data. These tools generally focus on movement modelling, but the steps required to clean raw data files from different tracking devices have been largely ignored. Such pre-processing steps are often time-consuming and involve a steep learning curve but are crucial for the creation of high-quality, standardised and shareable data. Moreover, decisions made at this early stage can substantially influence subsequent analyses, and in the current age of reproducibility crisis, the transparency of this process is vital. Here we present an open-access, reproducible toolkit written in the programming language R for processing raw data files into a single cleaned data set for analyses and upload to online tracking databases (found here: https://github.com/ExMove/ExMove). The toolkit comprises well-documented and flexible code to facilitate data processing and user understanding, both of which can increase user confidence and improve the uptake of sharing open and reproducible code. Additionally, we provide an overview website (found here: https://exmove.github.io/) and a Shiny app to help users visualise tracking data and assist with parameter determination during data cleaning. The toolkit is generalisable to different data formats and device types, uses modern 'tidy coding' practices, and relies on a few well-maintained packages. Among these, we perform spatial manipulations using the package sf. Overall, by collating all required steps from data collection to archiving on open access databases into a single, robust pipeline, our toolkit provides a valuable resource for anyone conducting animal movement analyses and represents an important step towards increased standardisation and reproducibility in animal movement ecology.
随着技术的不断进步,动物追踪研究的数量、类型和范围迅速增加。为此,开发了许多软件工具来分析动物运动数据。这些工具通常侧重于运动建模,但从不同追踪设备中清理原始数据文件所需的步骤在很大程度上被忽视了。这些预处理步骤通常很耗时,并且涉及陡峭的学习曲线,但对于创建高质量、标准化和可共享的数据至关重要。此外,在这个早期阶段做出的决策会极大地影响后续分析,在当前可重复性危机时代,该过程的透明度至关重要。在这里,我们提出了一个使用编程语言 R 编写的开源、可重复使用的工具包,用于将原始数据文件处理成单个清理数据集,以便进行分析并上传到在线追踪数据库(可在此处找到:https://github.com/ExMove/ExMove)。该工具包包含经过良好记录和灵活的代码,以促进数据处理和用户理解,这两者都可以提高用户的信心并提高开放和可重复使用代码的采用率。此外,我们提供了一个概述网站(可在此处找到:https://exmove.github.io/)和一个 Shiny 应用程序,以帮助用户可视化追踪数据并在数据清理过程中协助参数确定。该工具包可推广到不同的数据格式和设备类型,使用现代的“整洁编码”实践,并依赖于几个维护良好的包。其中,我们使用 sf 包进行空间操作。总的来说,通过将从数据收集到存档到开放访问数据库的所有必需步骤整理到单个稳健的管道中,我们的工具包为进行动物运动分析的任何人提供了有价值的资源,并代表着在动物运动生态学中实现标准化和可重复性的重要一步。