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https://github.com/mrc-ide/r21_vacc_antibody_model
https://github.com/mrc-ide/r21_vacc_antibody_model
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/mrc-ide/r21_vacc_antibody_model
- Owner: mrc-ide
- Created: 2023-10-05T11:00:54.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2023-11-16T09:53:54.000Z (about 1 year ago)
- Last Synced: 2024-04-23T15:34:24.893Z (8 months ago)
- Language: R
- Size: 7.08 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# R21/Matrix-M vaccine antibody and vaccine efficacy model
Code to
- estimate the association between antibody dynamics and vaccine efficacy against clinical malaria
of the R21/Matrix-M vaccine using Phase 2 trial data
- project the public health impact and cost-effectiveness of the R21/Matrix-M vaccine
As shown in: Schmit, Topazian et al. The public health impact and cost-effectiveness of the R21/Matrix-M malaria vaccine: a mathematical modelling study.
## Directory
```
.
├── ab_model # Scripts to estimate the dynamics of anti-CSP antibody titres
| ├── 1_fit_ab_model.R # Fit antibody model to immunogenicity data
| ├── 2_visualise_ab_model.R # Visualise and save parameter estimates from antibody model fit
| ├── ab_model.stan # Antibody model in STAN
| ├── output # Model outputs
| ├── R # Functions to run and fit model
| | ├── antibody_model.R # Antibody titre dynamics model
| | ├── draw_priors.R # Function to draw prior samples
| | ├── stan_utils.R # Helper functions
├── efficacy_model # Scripts to estimate the relationship between antibody titres and vaccine efficacy
| ├── 3_fit_efficacy_model.R # Fit efficacy model to case incidence data
| ├── 4_model_validation.R # Validate model against Phase 3 trial efficacy
| ├── data # Data files
| ├── output # Model outputs
| ├── R # Functions to run and fit model
| | ├── antibody_model.R # Antibody titre dynamics model
| | ├── efficacy_fitting.R # Functions for model fitting
| | ├── eq.R # Function for immunity and infection hazard
| | ├── hazard.R # Case incidence model
| | ├── season.R # Seasonality function
| | ├── utils.R # Helper functions
| | ├── vaccine_efficacy_model.R # Model for relationship between antibody titres and vaccine efficacy
├── malariasimulation_runs # Scripts to projecte public health impact and cost-effectiveness
| ├── 01_data # Data files
| ├── 02_code # Coding scripts
| | ├── data_and_libraries.R # Libraries
| | ├── A_parameter_draws.R # List parameters for each draw
| | ├── B_PfPR_EIR_match.R # Match PfPR to EIR
| | ├── C_HPC_runs.R # Model runs
| | ├── D_HPC_processing.R # Processing model runs
| | ├── Functions # Functions to simulate and calculate model outcomes
| | | ├── add_costs.R # Helper-functionadd costs
| | | ├── cost_effectiveness.R # Process CE
| | | ├── deaths_dalys.R # Helper-function calculate deaths & DALYs
| | | ├── generate_params.R # Generate dataframe of parameter lists
| | | ├── HPC_processing.R # Helper-function process model runs
| | | ├── outcome_averted.R # Helper-function calculate DALYs and cases averted
| | | ├── PRmatch.R # Calibrate model via EIR and PfPR
| | | ├── runsim.R # Run malariasimulation
| ├── 03_output # Model outputs
├── r21_vacc_antibody_model.Rproj # R.Studio project file
└── README.md # Project overview
```