https://github.com/epiforecasts/ebola-expert-interviews
Analysis of the results from interviews with experts regarding the spatial spread of Ebola in North-Kivu (2019/20)
https://github.com/epiforecasts/ebola-expert-interviews
Last synced: 10 months ago
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Analysis of the results from interviews with experts regarding the spatial spread of Ebola in North-Kivu (2019/20)
- Host: GitHub
- URL: https://github.com/epiforecasts/ebola-expert-interviews
- Owner: epiforecasts
- Created: 2024-03-08T09:23:34.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-03-13T17:02:56.000Z (about 2 years ago)
- Last Synced: 2025-07-25T12:45:16.832Z (11 months ago)
- Language: R
- Size: 28.5 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 3
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Metadata Files:
- Readme: README.md
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README
# Expert elicitation
Data and `R` code to support the expert elicitation analysis in *Forecasting the geographic spread of Ebola Virus Disease in the Democratic Republic of the Congo during the 2018-2020 outbreak*.
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### Study description
This study aims to forecast the geographic spread of the 2018-2020 Ebola Virus Disease outbreak in the DRC. The expert elicitation was conducted from December 2019 to March 2020, with a pilot study carried out in November 2019.
We describe the experts' responses and compare these to the cases reported.
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### Repository files
A description of each file and folder is provided below.
**Sourced scripts**
All script names starting by `00_` denote scrips that are not to be run alone but are sourced by other scripts.
* **`00_data_1.R`:** `R` script that inputs expert forecasts for November 2019 (pilot study) and outputs a .csv file with the results, stored in `Outputs`.
* **`00_data_2.R`:** `R` script that inputs expert forecasts for December 2019 and outputs 2 .csv files with the results: one including the additional health zones rated by the experts and one without, both stored in `Outputs`.
* **`00_data_3.R`:** `R` script that inputs expert forecasts for January 2020 and outputs 2 .csv files with the results: one including the additional health zones rated by the experts and one without, both stored in `Outputs`.
* **`00_data_4.R`:** `R` script that inputs expert forecasts for February 2020 and outputs 2 .csv files with the results: one including the additional health zones rated by the experts and one without, both stored in `Outputs`.
* **`00_data_5.R`:** `R` script that inputs expert forecasts for March 2020 and outputs 2 .csv files with the results: one including the additional health zones rated by the experts and one without, both stored in `Outputs`.
* **`00_data_cases.R`:** `R` script that reads in cases data.
* **`00_cumulative_calc.R`:** `R` script that inputs the raw data for all forecasts and outputs the cumulative data, stored in `Outputs`.
* **`00_plots.R`:** `R` script that inputs .csv files generated by `01_data.R` and `02_data_cumulative.R` and cases through `00_data_cases.R`, merges the data sets and generates plots, stored in `Plots`.
**Scripts to run**
* **`01_data.R`:** `R` script that sources scripts `00_data_1.R`, `00_data_2.R`, `00_data_3.R`, `00_data_4.R`, `00_data_5.R`and outputs .csv files, stored in `Outputs`.
* **`02_data_cumulative.R`:** `R` script that inputs .csv files generated by `01_data.R`, sources script `00_cumulative_calc.R` and outputs cumulative forecasts, stored as .csv files in `Outputs`.
* **`02_timeline.R`:** `R` script that inputs .csv file generated by `01_data.R` and outputs a plot of the time line of expert elicitations, stored in `Plots`.
* **`02_descriptive.R`:** `R` script that inputs .csv file generated by `01_data.R` and generates descriptive analysis for the results text.
* **`03_plots.R`:** `R` script that sources `00_plots.R` and makes plots for each month, stored in `Plots`.
**Folders**
* **`Outputs`:** a folder containing the expert elicitation forecasts needed for analysis generated by the `R` scripts.
+ `.csv` files entitled `results_month_year.csv` include only forecasts for the HZs rated by all experts,
+ `.csv` files entitled `results_month_year_additional_HZ.csv` include only forecasts for the HZs rated by some experts (in response to the follow-up question "any additional HZs with >1 case with >5% prob?")
+ `.csv` files entitled `results_month_year_cm.csv` include only the HZs rated by all experts with cumulative probabilities .
+ `.csv` file entitled `results_all.csv` includes all `.csv` files entitled `results_month_year.csv`
+ `.csv` file entitled `results_additional_HZ.csv` includes all `.csv` files entitled `results_month_year_additional_HZ.csv`
* **`Plots`:** a folder to save the figures generated by the `R` scripts.
**Project**
* **`Expert-elicitation.Rproj`:** An `RStudio` project file, to avoid having to set your working directory to the folder on your computer.
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Download the repository as a ZIP file using the green button *Clone or download* above, then open the .Rproj file in `RStudio` to begin.
The analysis was performed using R version 3.6.2 (2019-12-12).
For any issues with the code please contact [Alicia Roselló](https://www.lshtm.ac.uk/aboutus/people/rosello.alicia).