https://github.com/sepmein/vector_borne_disease_modelling
https://github.com/sepmein/vector_borne_disease_modelling
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/sepmein/vector_borne_disease_modelling
- Owner: sepmein
- Created: 2025-07-21T14:15:06.000Z (3 months ago)
- Default Branch: master
- Last Pushed: 2025-07-31T08:45:40.000Z (2 months ago)
- Last Synced: 2025-07-31T12:21:16.197Z (2 months ago)
- Language: R
- Size: 1.61 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Vector-Borne Disease Modelling: SEIR-SEI & Rt Estimation (R)
This project provides a modular R implementation for simulating and analyzing the transmission dynamics of vector-borne diseases（如登革热、基孔肯雅热）using a coupled SEIR model for humans and SEI model for vectors, and for estimating the real-time reproduction number (Rt) using EpiEstim.
## 文件结构
- `seir_dengue_model.R` — 主脚本，包含模型调用与示例
- `model_seir_SEI.R` — SEIR-SEI动力学模型定义
- `fit_incubation_distribution.R` — 潜伏期分布拟合与参数提取
- `estimate_rt_epiestim.R` — 用EpiEstim估算Rt
- `requirements.txt` — 依赖R包列表
- `README.md` — 项目说明文档
## 快速开始
1. 安装依赖包：
```r
install.packages(c('deSolve', 'ggplot2', 'reshape2', 'MASS', 'EpiEstim'))
```
2. 拟合潜伏期分布（如有原始数据）：
```r
source('fit_incubation_distribution.R')
# 输出均值、标准差、shape、rate等参数
```
3. 运行动力学模型：
```r
source('model_seir_SEI.R')
# 生成人群和蚊群的SEIR-SEI仿真结果
```
4. 估算实时再生数Rt：
```r
source('estimate_rt_epiestim.R')
# 生成Rt曲线
```
## 主要功能说明
### 1. 潜伏期分布拟合
- 支持伽马分布、对数正态分布等
- 自动输出均值、标准差、shape、rate等参数
- 结果可直接用于动力学模型参数设定
### 2. SEIR-SEI动力学模型
- 人群：SEIR结构
- 蚊群：SEI结构
- 参数可自定义，支持与分布拟合结果联动
- 输出各舱室人数随时间变化曲线
### 3. 实时再生数Rt估算
- 支持用模型输出或实际病例数据
- 采用EpiEstim包，支持自定义代间分布
- 输出Rt随时间变化曲线
## 参考资料
- [EpiEstim R包](https://cran.r-project.org/web/packages/EpiEstim/index.html)
- [deSolve R包](https://cran.r-project.org/web/packages/deSolve/index.html)
- [登革热/基孔肯雅热流行病学文献]
## 联系方式
如有问题或建议，请联系项目维护者。