Coral reef benthic and fish monitoring data from Turneffe Atoll, Belize, 2010-2023

Our dataset consists of data collected for four surveys (benthic point-intercept-method (PIM), benthic invertebrates, coral community, and reef fish) carried out at the Turneffe Atoll Marine Reserve in Belize, annually between the years of 2010-2018, and biennially between 2021-2023. For our annual surveys from 2010-2018, we followed the Mesoamerican Barrier Reef System Synoptic Monitoring Program (MBRS SMP) protocol1. For 2021 and 2023, our data collection followed the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol2-6. The change in protocol between 2018 and 2021 is due to the National adoption of the AGRRA protocol for coral reef monitoring in Belize7. The two protocols are very similar, as the MBRS SMP was based on AGRRA and Caribbean Coastal and Marine Productivity (CARICOMP) protocols1. Between 2010-2021, we archived our collected data in Excel sheets, stored locally at the UB-ERI. Under UB-ERI guidance, volunteers digitized the data, entering it into tabular data format from waterproof data collection sheets used in the field. In 2023, we transformed the data format according to tidy data principles8, and FAIR data principles9 using R Statistical Software10. We wrote custom validation rules in R, which allowed us to feed our data in and receive a report on any cell that violated a rule, such as a temperature measurement in Fahrenheit instead of Celcius. We then manually investigated each flagged cell to consider individually whether we should fix or exclude the measurement. Citations: Almada-Villela, P. C., Sale, P. F., Gold-Bouchot, G., & Kjerfve, B. (2003). Manual of methods for the MBRS synoptic monitoring program: Selected methods for monitoring physical and biological parameters for use in the Mesoamerican region (Protocol 4; p. 155). Mesoamerican Barrier Reef Systems Project. https://rris.biopama.org/sites/default/files/2021-03/MBRS%20synoptic%20monitoring.pdf Lang, J., Marks, K., Kramer, P., Kramer, P., & Ginsburg, R. (2010). Agrra protocols version 5.4. ReVision A Journal of Consciousness and Transformation. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016a). AGRRA Benthos Protocol. Summary Instructions. (Protocol Revision 2016-09-12; p. 3). Atlantic and Gulf Rapid Reef Assessment. https://www.agrra.org/wp-content/uploads/2016/06/AGRRA-Benthos-Protocol.pdf Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016b). AGGRA Detailed Fish Protocol. Instructions for Use, June 2016. (Revision 2016-09-12; p. 2). Atlantic and Gulf Rapid Reef Assessment. https://www.agrra.org/wp-content/uploads/2021/05/AGRRA-Fish-Protocol_June-2016.pdf AGRRA. (2021a). AGGRA Benthos Protocol. Summary Instructions, April 2021 Updated. (Revision 2021-04-12; p. 4). Ocean Research & Education. https://agrra.org/wp-content/uploads/2021/05/AGRRA-Benthos-Protocol-April_13_2021.pdf AGRRA. (2021b). AGGRA Coral Protocol. Summary Instructions, April 2021. (Revision 2021-04-12; p. 5). Ocean Research & Education. https://agrra.org/wp-content/uploads/2021/05/AGRRA-Coral-Protocol-April_13_2021.pdf McField, M., & Craig, N. (2018, February 28). Healthy Reefs letter to Belize Fisheries Department Wickham, H. (2014). Tidy Data. Journal of Statistical Software, 59(10). https://doi.org/10.18637/jss.v059.i10 Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1), 160018. https://doi.org/10.1038/sdata.2016.18 R Core Team. (2023). R: A Language and Environment for Statistical Computing (version 4.3.1) [Computer software]. R Foundation for Statistical Computing. https://www.R-project.org

本数据集包含于伯利兹特纳夫礁环礁海洋保护区（Turneffe Atoll Marine Reserve）内开展的四项调查所采集的数据，分别为底栖点截法（benthic point-intercept-method, PIM）、底栖无脊椎动物、珊瑚群落与礁岩鱼类调查。该调查于2010至2018年间每年开展一次，2021至2023年间每两年开展一次。

2010-2018年的年度调查遵循中美洲堡礁系统同步监测计划（Mesoamerican Barrier Reef System Synoptic Monitoring Program, MBRS SMP）规范1。2021年与2023年的数据采集则遵循大西洋与海湾快速礁岩评估（Atlantic and Gulf Rapid Reef Assessment, AGRRA）规范2-6。2018至2021年间监测规范变更的原因是伯利兹全国范围内采用了AGRRA珊瑚礁监测规范7。两项规范高度相似，因MBRS SMP的制定参考了AGRRA与加勒比沿海及海洋生产力（Caribbean Coastal and Marine Productivity, CARICOMP）规范1。

2010至2021年间，我们将采集的数据存档于Excel表格中，本地存储于UB-ERI。在UB-ERI的指导下，志愿者将野外使用的防水数据采集表中的内容数字化为表格数据格式。2023年，我们使用R统计软件（R Statistical Software）10，依据整洁数据原则（tidy data principles）8与FAIR数据原则（FAIR data principles）9对数据格式进行了标准化转换。我们在R中编写了自定义验证规则，可在导入数据后生成违规单元格报告，例如将温度测量值记录为华氏度而非摄氏度的情况。随后我们对每个标记的单元格逐一人工核查，以确定是否修正或剔除该测量值。

参考文献：
1. Almada-Villela, P. C., Sale, P. F., Gold-Bouchot, G., & Kjerfve, B. (2003). MBRS同步监测计划方法手册：中美洲区域物理与生物参数监测选定方法（规范4；第155页）。中美洲堡礁系统项目。https://rris.biopama.org/sites/default/files/2021-03/MBRS%20synoptic%20monitoring.pdf
2. Lang, J., Marks, K., Kramer, P., Kramer, P., & Ginsburg, R. (2010). AGRRA规范5.4版。《意识与转型期刊》（ReVision A Journal of Consciousness and Transformation）
3. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016a). AGRRA底栖生物规范：摘要指南（2016-09-12修订版；第3页）。大西洋与海湾快速礁岩评估项目。https://www.agrra.org/wp-content/uploads/2016/06/AGRRA-Benthos-Protocol.pdf
4. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016b). AGRRA鱼类详细调查规范：使用指南，2016年6月（2016-09-12修订版；第2页）。大西洋与海湾快速礁岩评估项目。https://www.agrra.org/wp-content/uploads/2021/05/AGRRA-Fish-Protocol_June-2016.pdf
5. AGRRA. (2021a). AGRRA底栖生物规范：摘要指南，2021年4月更新（2021-04-12修订版；第4页）。海洋研究与教育基金会。https://agrra.org/wp-content/uploads/2021/05/AGRRA-Benthos-Protocol-April_13_2021.pdf
6. AGRRA. (2021b). AGRRA珊瑚规范：摘要指南，2021年4月（2021-04-12修订版；第5页）。海洋研究与教育基金会。https://agrra.org/wp-content/uploads/2021/05/AGRRA-Coral-Protocol-April_13_2021.pdf
7. McField, M., & Craig, N. (2018, February 28). 致伯利兹渔业部的健康礁岩信函
8. Wickham, H. (2014). 整洁数据. 《统计软件期刊》, 59(10). https://doi.org/10.18637/jss.v059.i10
9. Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). 科学数据管理与托管FAIR指导原则. 《科学数据》, 3(1), 160018. https://doi.org/10.1038/sdata.2016.18
10. R Core Team. (2023). R：统计计算语言与环境（版本4.3.1）[计算机软件]. R统计计算基金会. https://www.R-project.org