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Automating report generation for disease surveillance data using R Markdown: a case study on mosquito surveillance data
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Chuangduan CHEN1, Shu XIAO2, 3, Jianpeng XIAO3, Ruipeng LU4, Zuhua RONG3, Weilin ZENG3, Jianguo ZHAO3, Dexin GONG3
Chinese Journal of Public Health | 2026, 42(2) : 205 - 211
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Chinese Journal of Public Health | 2026, 42(2): 205-211
• Survey and Report •
Automating report generation for disease surveillance data using R Markdown: a case study on mosquito surveillance data
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Chuangduan CHEN1, Shu XIAO2, 3, Jianpeng XIAO3, Ruipeng LU4, Zuhua RONG3, Weilin ZENG3, Jianguo ZHAO3, Dexin GONG3
Affiliations
  • 1Puning Municipal Center for Disease Control and Prevention, Jieyang 515300, China
  • 2School of Medicine, Jinan University, Guangzhou 510632, China
  • 3Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
  • 4Institute of Disinfection and Vector Control, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
Published: 2026-02-10 doi: 10.11847/zgggws1147047
Outline
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This study proposes a method for automated report generation in disease control agencies using R Markdown and demonstrates the entire workflow from data collection, analysis, and visualization to report generation through a case study on mosquito surveillance data. By integrating text, code, and output results, R Markdown significantly reduces manual operations and improves report accuracy and reproducibility. This study represents the first application of R Markdown in the automated report generation of mosquito surveillance, offering an efficient and reusable solution for public health. The findings highlight the method ability to enhance data processing efficiency, report flexibility, and real-time decision-making support.

R Markdown  /  automated report generation  /  disease surveillance  /  mosquito surveillance  /  data processing  /  visualization
陈创端, 肖树, 肖建鹏, 芦瑞鹏, 容祖华, 曾韦霖, 赵建国, 龚德鑫. 基于R Markdown文档的疾病监测报告自动化生成方法及应用：以蚊媒监测报告为例. 中国公共卫生, 2026 , 42 (2) : 205 -211 . DOI: 10.11847/zgggws1147047
Chuangduan CHEN, Shu XIAO, Jianpeng XIAO, Ruipeng LU, Zuhua RONG, Weilin ZENG, Jianguo ZHAO, Dexin GONG. Automating report generation for disease surveillance data using R Markdown: a case study on mosquito surveillance data[J]. Chinese Journal of Public Health, 2026 , 42 (2) : 205 -211 . DOI: 10.11847/zgggws1147047
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Year 2026 volume 42 Issue 2
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Article Info
doi: 10.11847/zgggws1147047
  • Receive Date：2025-02-07
  • Online Date：2026-10-23
  • Published：2026-02-10
Article Data
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History
  • Received：2025-02-07
  • Revised：2025-05-13
  • Accepted：2025-09-04
Affiliations
    1Puning Municipal Center for Disease Control and Prevention, Jieyang 515300, China
    2School of Medicine, Jinan University, Guangzhou 510632, China
    3Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
    4Institute of Disinfection and Vector Control, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China

Corresponding:

GONG Dexin, E-mail:
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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