The STRATEGIC study

This repository includes data and codes for reproducing the results of the manuscript:

"Strategies to inTerrupt RAbies Transmission for the Elimination Goal by 2030 In China (STRATEGIC): a modelling study"

In the following sections, we will describe the purposes of each major directory and the scripts in that folder. The scripts and data here are used for reproduction of the results in the paper only. Scripts were tested on R-4.0.5.

The analysis code is modified from the WHO rabies modelling consortium study

Reference: The Lancet Infectious Diseases 2019; 19(1): 102-11.

1.Analysis

The analysis .Rmd file is set to run the multivariate analysis and univariate analysis, and the results are saved at the output folder. If you want to run the codes, you need to:

1) Change the path

Please change the path to the location of the STRATEGIC folder you downloaded and run the first chunk to load the R function.

2) Prepare R packages

You may need to install the following R packages if you have not done so yet:

• triangle
• dplyr

Then you can run the second chunk to load the packages.

3) Load the data

Please run the third chunk to load the data needed for the analysis.

4) Probabilistic sensitivity analyses (PSA)

Please run the fourth chunk to complete the simulation of PSA (multivariate analysis).

5) One-way sensitivity analyses

Please run the fifth chunk to complete the simulation of univariate analysis.

2.Results prepare

The Results prepare.Rmd file is set to summarize the results from 2024-2035. The results will be saved in output folder.

3.Tables and figures generation

The plot .Rmd file is set to summarize the results of analysis. Tables and figures are saved at the figures and tables folder. If you want to run the codes, you need to:

1) Change the path

Please change the path to the location of the STRATEGIC folder you downloaded and run the first chunk to load the R function.

2) Prepare R packages

You may need to install the following R packages if you have not done so yet:

• dplyr
• tools
• ggplot2
• scales

And then you can run the second chunk to load the packages.

3) Generate tables

Please run the third to fifth chunk to generate the tables of the predicted human rabies deaths(Table 1 & 2), the incremental cost-effectiveness ratio (ICER) (Supplementary Table S5).

4) Generate figures

Please run the sixth to ninth chunk to generate the figures of the predicted human rabies deaths(Figure 2) and the cost effectiveness analysis(Figure 3), the one-way sensitivity analyses (Supplementary Figure S3), the probabilistic sensitivity analyses (Supplementary Figure S4).

If you are not interested in the details of this code, you can skip the following descriptions.

4.Descriptions of folders

Folder R

This folder contains major R functions used for our model fitting, parameter estimation and producing tables and figures.

• 1.rabies probability calculation.R: calculate the probability of the rabies infection of the person bitten by rabid dogs.
• 2.medical care probability calculation.R: calculate the probability to seek, receive and complete the medical care of the bitten person.
• 3.DALYs calculation.R: calculate the DALYs caused by human rabies.
• 4.time of strategy.R: prepare the simulation period of different strategies.
• 5.univariate analysis.R: simulate the one-way sensitivity analyses.
• 6.multivariate analysis.R: simulate the probabilistic sensitivity analyses.
• 7.results summary.R: summary the results of different scenarios by areas and years.
• 8.plot_function.R: prepare the results for tables & figures generation.

Folder data

This folder contains the main data used in the study.

• data.csv: This file contains human population, human-dog ratios, dog bite probabilities, medical care probabilities, and costs parameters.
• dogs_pop_traj.csv: This file contains dog population parameters.
• baseline_incidence.csv: This file contains rabies incidence of dogs.
• bio_data.csv: This file contains the prevented effect parameters of post-exposure prophylaxis (PEP) treatment.
• biological_param_p_infect.csv: This file contains probabilities of human rabies bitten on the different spots.
• DALY.csv: This file contains parameters used to estimate DALYs .
• lifetable.csv: This file contains life expectancy of different ages, used to calculate DALYs parameters.
• rabies_traj.csv: This file contains trends of rabies incidence caused by dog vaccination.
• vaccine_use.csv: This file contains parameters of completeness of the PEP regimen.

Folder output

This folder stores the results of analysis.Rmd and Results prepare.Rmd.

Folder figures and tables

This folder stores the files for main tables and figures.

• Tab1_model_summary_scenario.csv: This file presented Table 1 in the manuscript.
• Tab2_model_year_scenario_all.csv: This file presented Table 2 in the manuscript.
• Fig2_deaths_vaccinated_vials.pdf: This file presented Figure 2 in the manuscript.
• Fig3_ICER_province.pdf: This file presented Figure 3 in the manuscript.
• ICER_scenario.csv,multivariate.pdf,univariate.pdf presented results in the supplementary files.

(Update in Feb, 2023)

Folder additional analyses

This folder stores the data, code and results for the additional analysis. The code structure is basically the same as that of the main analysis.

• Folderdog vial price: This folder includes the cost constriant analysis of dog vial price, to find when the ICER of scenario 4c to be dominant, 1 time GDP per capita and 3 times GDP per capita.
  • Folder data contains the main data used in the study, same as the main analysis.
  • Folder R contains major R functions, same as the main analysis. We only replace the parameter dog_vial_price from a constant to a variable in the file 6.multivariate analysis.R, for the corresponding cost constriant analysis.
  • File analysis.Rmd is set to do the analysis of cost constriant analysis.
    • 1. Change the path
      • Please change the path to the location of the STRATEGIC folder you downloaded and run the first chunk to load the R function.
    • 2. Prepare R packages
      • You may need to install the following R packages if you have not done so yet:
        • triangle
        • dplyr
      • And then you can run the second chunk to load the packages.
    • 3. Load the data
      • Please run the third chunk to load the data needed for the analysis.
    • 4. Cost constriant analyses
      • Please run the fourth chunk to complete the cost constriant analyses. The result will show below the chunk.