GitHub - kevinvzandvoort/rotavirus_vaccine_efficacy: R-code to estimate (cumulative) rotavirus vaccine efficacy, using different assumptions about waning efficacy. Bayesian hierarchical models are implemented via Rjags to estimate cumulative vaccine efficacy, which is in turn converted to instantaneous vaccine efficacy.

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R-code to estimate (cumulative) rotavirus vaccine efficacy, using different assumptions about waning efficacy. Bayesian hierarchical models are implemented via Rjags to estimate cumulative vaccine efficacy, which is in turn converted to instantaneous vaccine efficacy.

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
cumVEtoInsFast.cpp		cumVEtoInsFast.cpp
functions.r		functions.r
prepare_extracted_data.r		prepare_extracted_data.r
process_modelled_results.r		process_modelled_results.r
r_models_pooled.r		r_models_pooled.r
readme.txt		readme.txt
rjags_models_indonesia.r		rjags_models_indonesia.r
rjags_models_pooled.r		rjags_models_pooled.r
rotavirus_vaccine_efficacy_extracted.csv		rotavirus_vaccine_efficacy_extracted.csv
rotavirus_vaccine_efficacy_index.r		rotavirus_vaccine_efficacy_index.r
run_rjags_model.r		run_rjags_model.r

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This repository is supplemental to the paper: Efficacy of live oral rotavirus vaccines by duration of follow-up: a meta-regression of randomised controlled trials. https://doi.org/10.1016/S1473-3099(19)30126-4

DATA
The data for the pooled analysis is provided in rotavirus_vaccine_efficacy_extracted.csv

CODE
The main script is provided in rotavirus_vaccine_efficacy_index.r
This script sources multiple other scripts:
- functions.r
  * loads a number of helper functions used to show the results of the analysis
- process_modelled_results.r
  * takes the extracted data-points and re-calculates the relative risk and VE in each study
- rjags_models_pooled.r
  * the models that were fitted to the data in the pooled analysis (in Rjags language)
- r_models_pooled.r
  * the (same) models that were fitted to the data in the pooled analysis (in R language)
- rjags_models_indonesia.r
  * the (same) models that were fitted to the data in the re-analysis of the RV3-BB Indonesia trial
- run_rjags_model.r
  * runs the model in Rjags
- process_modelled_results.r
  * processes the posterior estimated with Rjags
  * calculates VE and iVE for each posterior sample
    ** provides median and 95% credible intervals