Data and code from paper: The carbon sink of secondary and degraded humid tropical forests

This repository contains the data and code produced for the following paper: <strong>Title: </strong>The carbon sink of recovering secondary and degraded humid tropical forests <strong>Contact:</strong> Viola Heinrich ([e-mail]) <strong>Please note:</strong> throughout repository where files include reference to: &lt;...<strong>congo_basin</strong>...&gt; this refers to the <strong>Central Africa </strong>region as it is termed in the main paper. the <strong>code</strong> <strong>has not been amended</strong> for wider use and still contains set working directories for use with University of Bristol systems, you will need to change these for the scripts to run. The data produced in this project were produced using a combination of programming languages due to differences in the author's preferences and expertise. Overall, the initial data analysis was carried out in (i) Google Earth Engine, and (ii) Arcpy (Python3.6.10). Most of the post-processing of the initial data was then carried out in <strong>R (v3.6) for which the code and output datasets are available here.</strong> To access the code used in <strong>Google Earth Engine</strong> that was used to produce and export data from the Tropical Moist Forest dataset (e.g. Years Since Last Disturbance of secondary/degraded forest), please follow the link: https://code.earthengine.google.com/d303fc21e7b57a8fc259e0ee2b58bfb4 This repository contains the following zipped folders: <strong>data_folder</strong>: this folder contains further folders with all the data produced for this paper. Fig1_data_models: All data needed to produce Figure 1 of the main paper, including an .RDS version of the 6 main regrowth models produced for this paper (secondary and degraded forests in the three regions). These are the files beginning with "<strong>regrowthModel_..RDS</strong>. Additionally, the folder includes the dataframe files originally from GeoTiff files that were used to extract the Aboveground Biomass in old-growth (undisturbed forests) &gt; e.g. the subfolder "amazon_basin_oldG_AGB" contains the .dbf files representing the AGB in old-growth forest pixels. There are 4 files as the Amazon was split up into 4 sections for computational reasons. Similarly, the Central Africa region (here referred to as congo_basin) was split up into 2 regions. Fig2_data_models_plus_exFig3_to_5: The data needed to produce Figure 2 in the main paper as well as the Extended Data Figures 3 to 5. This includes .RDS versions of the regrowth models for secondary and degraded forests in the three regions for the different variables considered (files beginning with "<strong>regrowthModel_..RDS</strong>) e.g. "regrowtModel_borneo_deg_MaxTemo_low.rds", refers to the regrowth model shown in Figure 2c - the regrowth model for Bornean degraded forests for the variable "Maximum Temperature", where "low" refers to the lowest temperature range considered in the study. As before, files are provided giving information on the AGB in old-growth forests for each region within different conditions of each driving variable. Fig4: All the data needed to produce Figure 4 (and Supplementary Figure 18) of the main paper. This includes the file "regrowth_in_all_basins_by_country_input_data.csv", which contains data on the total number of cells for each forest type for each Years Since Last Disturbance (YSLD) in each region. Extended_dataFig1_input: The input for Extended Data Figure 1, including the values derived from other studies used in this comparison as well as additional notes/comments on how the data were assessed. Extended_dataFig2_input: the input data used to determine the standardised coefficients seen in the Extended Data Figure 2. Extended_data_table_inputs: The inputs for the Extended Data Tables 1 and 2. Inputs include the dataframe files (.dbf), of key variables that were extracted from the GeoTiff files. Only the .dbf files have been included here to limit excessively large data being uploaded. <strong>code_folder.zip</strong>: The code in this folder was used to produce the main figures and results for the extended data tables shown in the paper. this folder also contains a file "example_code_read_in_models.R" which provides an example of how best to read in the regrowth models for each region and forest type to extract important information such as the: (i) average growth rate in the first 20 years of analysis, (ii) all AGCs as a function of YSLD, and (iii) the estimated time it takes to reach the asymptote. <strong>Data and Code usage:</strong> When using any code or data in this repository or another related to this study please cite Heinrich et al. and the original paper as well as the DOI of this repository. Further source data in .xlsx format were also submitted with the main manuscript. If you need anything else, please contact the corresponding author: Viola Heinrich ([e-mail])本仓库包含为以下论文研发的数据与代码：<strong>论文标题：</strong>恢复中次生与退化湿润热带森林的碳汇功能 <strong>联系方式：</strong>Viola Heinrich（[e-mail]） <strong>请注意：</strong>本仓库内所有带有`&lt;...<strong>congo_basin</strong>...&gt;`标识的文件，均对应正文中所称的<strong>中非地区</strong>。 本仓库的<strong>代码未针对通用使用场景进行适配调整</strong>，仍保留了布里斯托大学服务器环境下预设的工作目录，使用者需自行修改相关配置以确保脚本可正常运行。 由于作者的研究偏好与专业背景差异，本项目的数据处理采用了多种编程语言完成。整体而言，初始数据分析工作通过以下工具完成：(i) 谷歌地球引擎（Google Earth Engine），(ii) Arcpy（Python 3.6.10）。初始数据的大部分后处理工作则在<strong>R语言（v3.6版本）</strong>环境中完成，相关代码与输出数据集已存放于本仓库。 若需获取用于生成并导出热带湿润森林数据集（例如次生/退化森林的最后扰动年份（Years Since Last Disturbance，YSLD））的<strong>谷歌地球引擎</strong>代码，请访问以下链接：https://code.earthengine.google.com/d303fc21e7b57a8fc259e0ee2b58bfb4 本仓库包含以下压缩文件夹： <strong>data_folder</strong>：该文件夹内包含多个子目录，存储了本论文所需的全部产出数据。 Fig1_data_models：存放用于绘制正文中图1的全部数据，包含本论文研发的6个主要再生模型的.RDS格式文件（对应三大区域的次生与退化森林），此类文件均以<strong>regrowthModel_..RDS</strong>为前缀。此外，该文件夹还包含从GeoTiff文件中提取得到的dataframe文件，用于获取原始林（未受干扰森林）的地上生物量（Aboveground Biomass，AGB）。例如子文件夹`amazon_basin_oldG_AGB`内存储了代表原始林像素地上生物量的.dbf文件，由于计算资源限制，亚马逊流域被划分为4个分区，因此共包含4个此类文件。同理，中非地区（本仓库内以`congo_basin`指代）也被划分为2个分区。 Fig2_data_models_plus_exFig3_to_5：存放用于绘制正文中图2以及扩展数据图3至5的全部数据。其中包含针对三大区域次生与退化森林、不同驱动变量的再生模型.RDS格式文件（文件名以<strong>regrowthModel_..RDS</strong>为前缀）。例如文件`regrowtModel_borneo_deg_MaxTemo_low.rds`对应图2c所示的模型：即针对婆罗洲退化森林、以“最高气温”为驱动变量的再生模型，其中“low”代表本研究中纳入的最低气温区间。与前文一致，该文件夹还提供了各区域在不同驱动变量条件下的原始林地上生物量数据文件。 Fig4：存放用于绘制正文中图4（及补充图18）的全部数据。其中包含文件`regrowth_in_all_basins_by_country_input_data.csv`，该文件记录了各区域内每类森林类型在不同最后扰动年份（YSLD）下的总像元数。 Extended_dataFig1_input：存放扩展数据图1的输入数据，包含本研究对比分析所用的其他研究的衍生数值，以及关于数据评估方法的补充说明。 Extended_dataFig2_input：存放用于计算扩展数据图2中标准化系数的输入数据。 Extended_data_table_inputs：存放扩展数据表1与2的输入数据。此类输入数据包含从GeoTiff文件中提取的关键变量dataframe文件（.dbf格式）。为控制上传文件体积，本文件夹仅包含.dbf格式文件。 <strong>code_folder.zip</strong>：该压缩包内的代码用于生成论文中的主图以及扩展数据表的结果。此外，文件夹内还包含文件`example_code_read_in_models.R`，该示例代码演示了如何读取各区域、各森林类型的再生模型，以提取三类关键信息：(i) 分析前20年的平均生长速率；(ii) 以最后扰动年份为变量的总地上碳储量（Aboveground Carbon，AGC）；(iii) 达到生长渐近线所需的预估时间。 <strong>数据与代码使用规范：</strong>若使用本仓库或本研究相关仓库中的代码与数据，请引用Heinrich等人的原创论文以及本仓库的DOI。本研究的补充源数据以.xlsx格式随主稿件一同提交。若有其他需求，请联系通讯作者Viola Heinrich（[e-mail]）