Animation of tagged southern right whale and vessel traffic

This animation, embedded in the html, shows the satellite tag derived movements of the southern right whale (black track) and the Automatic Identification System (AIS) derived movements of vessels in the region (red tracks; Australian Marine Safety Authority Craft Tracking System). The whale track was interpolated to match the hourly time stamp of the AIS data (see Methods and Materials: Satellite sensor, track and ship movement analysis). The date and time for each frame (top, centre) is 'year-month-day hour:min:sec' in UTC.As part of a multi-year study of inshore movements and offshore foraging ground locations, we biopsied and satellite tagged southern right whales in Flinders Bay, Augusta, Western Australia in September 2022. Here we focus on a female with calf tagged on 9 September 2022. A transdermal Wildlife Computer SPOT-372 satellite tag that provides data on location and water temperature was deployed. To account for the spatial error associated with satellite tag derived Argos locations, we fitted a correlated random walk model using the fit_ssm function from the R package aniMotum (Jonsen et al., 2023) and estimated new locations at each of the original observed Argos location times. Travel speed was calculated using the distance (distanceTrack function from the argosfilter package; Freitas et al., 2008) and the time difference (difftime function in base R) between two consecutive locations. Vessel tracking data were downloaded from the Australian Marine Safety Authority (AMSA) Craft Tracking System (CTS). CTS collects vessel traffic data from a variety of sources, including terrestrial and satellite shipborne Automatic Identification System (AIS) data sources. We extracted vessel traffic data for the months from May to November 2022. The dataset covers the extent of Australia’s Search and Rescue Region. The southern right whale track was interpolated to match the hourly time stamp of the AIS data using the align_move function (package: moveVis (version: 0.10.5; Schwalb-Willmann et al., 2020)) and the distance between the whale and vessel locations calculated using the pointDistance function (package: raster (Hijmans R, 2023)) in R. Jonsen, I.D., Grecian, W.J., Phillips, L., Carroll, G., McMahon, C., Harcourt, R.G., Hindell, M.A., and Patterson, T.A. (2023). aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation. Methods Ecol. Evol. 14(3): 806-816. [Available at: https://doi.org/10.1111/2041-210X.14060] Freitas, C., Lydersen, C., Fedak, M., and Kovacs, K.M. (2008). A simple new algorithm to filter marine mammal Argos locations. Mar. Mammal Sci. 24: 315-325. [Available at: https://doi.org/10.1111/j.1748-7692.2007.00180.x] Schwalb-Willmann, J., Remelgado, R., Safi, K., and Wegmann, M. (2020). moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in R. Methods. Ecol. Evol. 11: 664-669. [Available at: https://doi.org/10.1111/2041-210X.13374] Hijmans, R.J. (2023). raster: Geographic Data Analysis and Modeling. R package version 3.6-26. Also see 'Harcourt, R., Sprogis, K., Gales, N.J., Andrews-Goff, V., Double, M., Besier, S., Riekkola, L., and Carrol, E.L. (2025). Stranding of a satellite-tagged southern right whale off southwest Australia. J. Cetacean Res. Manage. Special Issue 5: 45-64' for further detail.

嵌入HTML文档的动画展示了南露脊鲸的卫星标签追踪运动轨迹（黑色轨迹），以及该区域内船舶的自动识别系统（Automatic Identification System, AIS）运动轨迹（红色轨迹；数据来自澳大利亚海事安全局船舶追踪系统）。鲸类轨迹经插值处理，以匹配AIS数据的小时时间戳（详见《方法与材料：卫星传感器、轨迹与船舶运动分析》章节）。每一帧画面的日期和时间（位于画面顶部中央）采用协调世界时（UTC）格式，标注为「年-月-日 时:分:秒」。

本研究为关于近岸活动与近海觅食地位置的多年期研究的一部分，我们于2022年9月在澳大利亚西部奥古斯塔的弗林德斯湾（Flinders Bay）对南露脊鲸实施皮肤活检并部署卫星追踪标签。本数据集聚焦于2022年9月9日标记的一头携带幼崽的雌性南露脊鲸。我们部署了一款透皮式Wildlife Computer SPOT-372卫星标签，该标签可采集位置与水温数据。

为校正卫星标签衍生的阿尔戈斯（Argos）定位数据所附带的空间误差，我们使用R语言aniMotum扩展包（Jonsen等，2023）中的fit_ssm函数构建了相关随机游走模型，并在原始观测的所有Argos定位时刻估算了新的定位坐标。移动速度通过相邻两个定位点之间的距离（使用argosfilter扩展包的distanceTrack函数；Freitas等，2008）与时间差（基础R语言的difftime函数）计算得出。

船舶追踪数据下载自澳大利亚海事安全局（Australian Marine Safety Authority, AMSA）船舶追踪系统（Craft Tracking System, CTS）。CTS从多种数据源采集船舶交通数据，包括地面与星载AIS数据源。我们提取了2022年5月至11月的船舶交通数据，数据集覆盖澳大利亚搜救区域全域。

我们使用R语言moveVis扩展包（版本0.10.5；Schwalb-Willmann等，2020）中的align_move函数，将南露脊鲸的轨迹进行插值处理以匹配AIS数据的小时时间戳，并使用R语言raster扩展包（Hijmans R, 2023）中的pointDistance函数计算鲸类与船舶定位点之间的距离。

### 参考文献
1. Jonsen, I.D., Grecian, W.J., Phillips, L., Carroll, G., McMahon, C., Harcourt, R.G., Hindell, M.A., and Patterson, T.A. (2023). aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation. 《生态学与进化方法》, 14(3): 806-816. [可访问：https://doi.org/10.1111/2041-210X.14060]
2. Freitas, C., Lydersen, C., Fedak, M., and Kovacs, K.M. (2008). A simple new algorithm to filter marine mammal Argos locations. 《海洋哺乳动物科学》, 24: 315-325. [可访问：https://doi.org/10.1111/j.1748-7692.2007.00180.x]
3. Schwalb-Willmann, J., Remelgado, R., Safi, K., and Wegmann, M. (2020). moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in R. 《生态学与进化方法》, 11: 664-669. [可访问：https://doi.org/10.1111/2041-210X.13374]
4. Hijmans, R.J. (2023). raster: Geographic Data Analysis and Modeling. R包版本3.6-26.

如需更多研究细节，可参考：Harcourt, R., Sprogis, K., Gales, N.J., Andrews-Goff, V., Double, M., Besier, S., Riekkola, L., and Carrol, E.L. (2025). Stranding of a satellite-tagged southern right whale off southwest Australia. 《鲸类研究与管理杂志》特刊第5期: 45-64.