Configuration files for the ED2 simulations for the Brazilian Amazon, initialised with airborne lidar

This data set contains the configurations for the ED2 simulations presented in the following manuscript: Longo, M., M. Keller, L. M. Kueppers, K. Bowman, O. Csillik, A. Ferraz, P. R. Moorcroft, J. P. Ometto, B. S. Soares-Filho, X. Xu, M. L. F. de Assis, E. B. Görgens, E. J. L. Larson, J. F. Needham, E. M. Ordway, F. R. S. Pereira, E. Rangel Pinagé, L. Sato, L. Xu and S. Saatchi. Degradation and deforestation increase the sensitivity of the Amazon Forest to climate extremes. In review. The configurations are organised into five compressed folders, corresponding to the simulation steps. R001_BrAmaz_s1c1t1l0f0.tgz. This is the spin up step of simulation R006_BrAmaz_s1c0t1l0f0 (Recovery in the manuscript). These runs were initialised with airborne lidar data and run with vegetation dynamics enabled and natural disturbance only. The final step of this result became the initial condition for R006_BrAmaz_s1c0t1l0f0 (Recovery), but otherwise this simulation was not analysed in the manuscript. R003_BrAmaz_s1c1t1l1f0.tgz. This is the spin up step of simulation R005_BrAmaz_s1c0t1l1f0 (Degradation in the manuscript). These runs were initialised with airborne lidar data and run with vegetation dynamics enabled and natural disturbance and anthropogenic disturbances. The final step of this result became the initial condition for R005_BrAmaz_s1c0t1l1f0 (Degradation), but otherwise this simulation was not analysed in the manuscript. R004_BrAmaz_s1c0t0l0f0.tgz. This is the simulation Control in the manuscript. This simulation was initialised with airborne lidar forest structure and run with vegetation dynamics disabled. The results of this simulation were presented in the manuscript. R005_BrAmaz_s1c0t1l1f0.tgz. This is the simulation Degradation in the manuscript. This simulation was initialised with the last time step of simulation R003_BrAmaz_s1c1t1l1f0, and run with vegetation dynamics disabled. The results of this simulation were presented in the manuscript. R006_BrAmaz_s1c0t1l0f0.tgz. This is the simulation Recovery in the manuscript. This simulation was initialised with the last time step of simulation R001_BrAmaz_s1c1t1l0f0, and run with vegetation dynamics disabled. The results of this simulation were presented in the manuscript. The initial conditions and boundary conditions are provided in the linked archives. In addition, in each directory, there are 350 sub-directories with a name structure that follows this example: ta0006_lon-60.50_lat-12.50_ifire00. In this example, ta0006 is the grid cell ID 0006, and lon-60.50 and lat-12.50 are the coordinates of the grid cell centre (60.5°W; 12.5°S, respectively). The key ifire00 is always zero, as a reminder that fires were disabled in all runs. . In addition, each dire ED2IN. This is the namelist used for the simulation of each individual grid cell. For additional information on the namelist variables, check the ED2 Wiki page. read_monthly.r. This script reads in the analysis output files, carries out some minimal processing of the monthly averages (e.g., unit conversion, simple aggregations), and saves R objects. These scripts require the folder Rsc (also provided, see below), and multiple packages. The script is old, so in case packages are missing and cannot be installed, try commenting out the package in Rsc/load.everything.r, because they may not be needed. The one obsolete package that is required is R package hdf5, which is also provided (see below). histo. This directory contains the first and last history (restart) files generated by the simulation. In addition, the following files are provided outside the sub-folder structure 01_regional_gridded.r. This script concatenates the RData objects from each individual run, and creates a single RData file for each simulation, with a subset of variables of interest. These scripts require the folder Rsc (also provided, see below), and multiple packages. The script is old, so in case packages are missing and cannot be installed, try commenting out the package in Rsc/load.everything.r, because they may not be needed Rsc.tgz. A suite of R scripts that may be called by read_monthly.r or 01_regional_gridded.r. Make sure the correct path is given in read_monthly.r or 01_regional_gridded.r scripts, and these scripts should be automatically loaded. hdf5_1.6.12.tar.gz. This is the source code of the now obsolete hdf5 R package. To install it, start an R session, set the working directory to be the same path where hdf5_1.6.12.tar.gz is located, and run the following command: install.packages(“hdf5_1.6.12.tar.gz”,repos=NULL). Additional configuration may be needed if the C compiler and/or the hdf5 libraries are not in default locations.本数据集包含下述论文中呈现的ED2模拟的配置文件： Longo, M.、M. Keller、L. M. Kueppers、K. Bowman、O. Csillik、A. Ferraz、P. R. Moorcroft、J. P. Ometto、B. S. Soares-Filho、X. Xu、M. L. F. de Assis、E. B. Görgens、E. J. L. Larson、J. F. Needham、E. M. Ordway、F. R. S. Pereira、E. Rangel Pinagé、L. Sato、L. Xu 及 S. Saatchi. 《森林退化与砍伐加剧亚马孙森林对极端气候的敏感性》，已投稿待审。 配置文件被整理为5个压缩文件夹，分别对应模拟步骤： 1. R001_BrAmaz_s1c1t1l0f0.tgz：该文件为模拟R006_BrAmaz_s1c0t1l0f0（即论文中的恢复场景Recovery）的自旋启动阶段。本模拟以机载激光雷达（airborne lidar）数据初始化，开启植被动态模拟，仅考虑自然干扰。其最终结果的时间步长被用作R006_BrAmaz_s1c0t1l0f0（恢复场景）的初始条件，但本模拟本身未在论文中进行分析。 2. R003_BrAmaz_s1c1t1l1f0.tgz：该文件为模拟R005_BrAmaz_s1c0t1l1f0（即论文中的退化场景Degradation）的自旋启动阶段。本模拟以机载激光雷达数据初始化，开启植被动态模拟，同时考虑自然干扰与人为干扰。其最终结果的时间步长被用作R005_BrAmaz_s1c0t1l1f0（退化场景）的初始条件，但本模拟本身未在论文中进行分析。 3. R004_BrAmaz_s1c0t0l0f0.tgz：即论文中的对照模拟Control。本模拟以机载激光雷达获取的森林结构数据初始化，关闭植被动态模拟，其结果已在论文中呈现。 4. R005_BrAmaz_s1c0t1l1f0.tgz：即论文中的退化场景模拟。本模拟以R003_BrAmaz_s1c1t1l1f0的最终时间步长作为初始条件，关闭植被动态模拟，其结果已在论文中呈现。 5. R006_BrAmaz_s1c0t1l0f0.tgz：即论文中的恢复场景模拟。本模拟以R001_BrAmaz_s1c1t1l0f0的最终时间步长作为初始条件，关闭植被动态模拟，其结果已在论文中呈现。 初始条件与边界条件已在关联归档文件中提供。此外，每个目录下包含350个子目录，其命名格式遵循如下示例：`ta0006_lon-60.50_lat-12.50_ifire00`。本示例中，`ta0006`代表网格单元ID为0006，`lon-60.50`与`lat-12.50`分别代表网格单元中心的坐标（西经60.5°，南纬12.5°）。关键标识`ifire00`始终为0，用以提醒所有模拟均未启用火灾模拟。 ED2IN：该文件为每个独立网格单元的模拟所用的namelist（namelist）配置文件。如需了解namelist变量的更多信息，请查阅ED2 Wiki页面。 read_monthly.r：该脚本用于读取分析输出文件，对月均数据进行简单处理（例如单位转换、简易聚合），并保存R对象。本脚本依赖Rsc文件夹（亦随数据集提供，详见下文）以及多个R包。因脚本年代较久，若出现依赖包缺失且无法安装的情况，可尝试在Rsc/load.everything.r中注释掉对应包，因为部分包可能并非必需。唯一必须的过时R包为hdf5，该包的源码亦随数据集提供（详见下文）。 histo目录：该目录包含模拟生成的首个与最后一个历史（重启）文件。 此外，子文件夹结构外还提供以下文件： 01_regional_gridded.r：该脚本用于合并各独立模拟运行的RData对象，并为每个模拟生成单个RData文件，仅保留感兴趣的变量子集。本脚本同样依赖Rsc文件夹以及多个R包。因脚本年代较久，若出现依赖包缺失无法安装的情况，可在Rsc/load.everything.r中注释掉对应包，部分包可能并非必需。 Rsc.tgz：一套可供read_monthly.r或01_regional_gridded.r调用的R脚本。请确保在read_monthly.r或01_regional_gridded.r脚本中配置了正确的路径，即可自动加载这些脚本。 hdf5_1.6.12.tar.gz：该文件为现已过时的hdf5 R包的源码。安装方法为：启动R会话，将工作目录设置至该压缩包所在路径，运行命令`install.packages("hdf5_1.6.12.tar.gz", repos=NULL)`。若C编译器或hdf5库未处于默认路径，则可能需要额外配置。