EcoTroph-Dyn unexploited ecosystems

R scripts to run the EcoTroph-Dyn model in a theoretically unexploited ecosystem and analyze climate change effects. WARNING: In this repository, you will find an original implementation of the EcoTroph_Dynamic modelling framework, which is completely independent of the EcoTroph Package (https://cran.r-project.org/web/packages/EcoTroph/index.html). EcoTroph-Dyn is a simplified semi-empirical model of the flow of biomass through the food web, from primary producers to top predators (Gascuel 2005, Gascuel et al. 2011). It has been used in particulate to assess the ecosytem impact of fishing. In this implementation of EcoTroph-Dyn, biomass and production of upper trophic levels (at each trophic level) are calculated based on the trophic transfer efficiency and the flow kinetic at each trophic level, using sea water temperature, net primary production and transfer efficiency of high trophic levels (see du Pontavice et al 2021 https://doi.org/10.1111/gcb.15576) as the model inputs. The details and the theoretical basis about the implementation of EcoTroph-Dynamic available in this repository would be presented in Guibourd de luzinais et al. (2024). How to run those scripts? 1.Open the R script: EcoTroph_Dynamic_core_function.R. 2. Run the first lines and the fonctions called "create_data_envi",and "ecotroph_dynamic_core". 3. Use ecotroph with the examples at the end of the script (3 examples) or use your own data following the details in the R script. REFERENCES Du Pontavice, H., Gascuel, D., Reygondeau, G., Stock, C., & Cheung, W. W. L. (2021). Climate‐induced decrease in biomass flow in marine food webs may severely affect predators and ecosystem production. Global Change Biology, 27(11), 2608–2622. https://doi.org/10.1111/gcb.15576. Gascuel, D., Bozec, Y.-M., Chassot, E., Colomb, A., & Laurans, M. (2005). The trophic spectrum: Theory and application as an ecosystem indicator. ICES Journal of Marine Science, 62(3), 443–452. https://doi.org/10.1016/j.icesjms.2004.12.013. Gascuel, D., Guenette, S. & Pauly, D. (2011). The trophic-level-based ecosystem modelling approach: theoretical overview and practical uses. ICES J. Mar. Sci.. DOI: https://doi.org/10.1093/icesjms/fsr062. Guibourd de Luzinais, V., Gascuel, D., Reygondeau, G., D., & Cheung, W. W. L. (2024). Large potential impacts of Marine Heatwaves on ecosystem functioning. manuscript submitted for publication in Global Change Biology.

用于在理论上未开发的生态系统中运行EcoTroph-Dyn模型，并分析气候变化影响的R脚本。
警告：本仓库包含EcoTroph动态建模框架的原创实现，该实现完全独立于EcoTroph软件包（https://cran.r-project.org/web/packages/EcoTroph/index.html）。

EcoTroph-Dyn是一款简化的半经验模型，用于描述从初级生产者（primary producers）到顶级捕食者（top predators）的食物网（food web）生物量（biomass）流动过程（Gascuel, 2005；Gascuel等, 2011）。该模型此前尤其被用于评估捕捞活动对生态系统的影响。

在本实现的EcoTroph-Dyn模型中，各营养级（trophic level）上层的生物量与产量将基于各营养级的营养传递效率（trophic transfer efficiency）与流动动力学进行计算，模型输入参数包括海水温度、净初级生产力（net primary production）以及高营养级的传递效率（详见du Pontavice等, 2021：https://doi.org/10.1111/gcb.15576）。

本仓库中关于EcoTroph动态建模框架实现的细节与理论基础，将在Guibourd de Luzinais等（2024）的研究中详细阐述。

如何运行这些脚本？
1. 打开R脚本：`EcoTroph_Dynamic_core_function.R`。
2. 运行脚本的前置代码以及名为`create_data_envi`和`ecotroph_dynamic_core`的函数。
3. 可使用脚本末尾附带的3个示例进行模型调用，或根据R脚本中的说明使用自定义数据。

参考文献
Du Pontavice, H., Gascuel, D., Reygondeau, G., Stock, C., & Cheung, W. W. L. (2021). 气候变化诱导的海洋食物网生物量流动减少可能严重影响捕食者与生态系统生产力. 全球变化生物学（Global Change Biology）, 27(11), 2608–2622. https://doi.org/10.1111/gcb.15576.
Gascuel, D., Bozec, Y.-M., Chassot, E., Colomb, A., & Laurans, M. (2005). 营养谱：作为生态系统指示物的理论与应用. 国际海洋考察理事会海洋科学杂志（ICES Journal of Marine Science）, 62(3), 443–452. https://doi.org/10.1016/j.icesjms.2004.12.013.
Gascuel, D., Guenette, S. & Pauly, D. (2011). 基于营养级的生态系统建模方法：理论概述与实践应用. 国际海洋考察理事会海洋科学杂志（ICES J. Mar. Sci.）. DOI: https://doi.org/10.1093/icesjms/fsr062.
Guibourd de Luzinais, V., Gascuel, D., Reygondeau, G., & Cheung, W. W. L. (2024). 海洋热浪对生态系统功能的潜在巨大影响. 投稿于《全球变化生物学》的待发表手稿。