Cascades of effectiveness of new-generation insecticide-treated nets against malaria, from entomological trials to real-life conditions
This code is associated with the following manuscript:
Cascades of effectiveness of new-generation insecticide-treated nets against malaria, from entomological trials to real-life conditions
Clara Champagne, Jeanne Lemant, Alphonce Assenga, Ummi A. Kibondo, Ruth G. Lekundayo, Emmanuel Mbuba, Jason Moore, Joseph B. Muganga, Watson S. Ntabaliba, Olukayode G. Odufuwa, Johnson Kyeba Swai, Maria Alexa, Roland Goers, Monica Golumbeanu, Nakul Chitnis, Amanda Ross, Sarah Moore, Emilie Pothin
The user should refer to the manuscript for methodological details. Additionally, a dashboard to explore the results is available here.
The code is structured in two folders:
- EHT_fit: includes the code for the statistical analysis of Experimental Hut Trial data, as well as for building effectiveness cascades
- RCT_validation: includes the code for mathematical modelling of Randomized Controlled Trials with OpenMalaria
The main scripts to be executed in that order are the following:
- 1_Data_formatting: contains the code used to process the input EHT data, convert it into the proper format for inference, and compute descriptive statistics
- 2_EHT_fitting_multinomial: contains the code to perform the statistical inference as well as provide the effectiveness cascades
- 3_convergence_diagnostics: contains the convergence diagnostics for MCMC outputs with stan
- 4_create_inputs_dasboards: formats and summarises the outputs for the dashboard
Other scripts are functions to be sourced while running the analysis.
The main scripts to be executed in that order are the following:
- 1_seasonality: contains the code used to export seasonality patterns from CHIRPS
- 2a_fit_ITNcov_mosha and 2b_fit_ITNcov_protopopoff: contains the code to compute functional survival and net durability parameters for each RCT
- 3a_RCT_mosha_controlArm and 3b_RCT_protopopoff_controlArm: contains the code required to run OpenMalaria for the control arms of each RCT
- 4a_RCT_mosha_interventionArms and 4b_RCT_protopopoff_interventionArms: contains the code required to run OpenMalaria for the intervention arms of each RCT (validation)
- 5a_validation_final_plot: contains the code for final visualisation of the results as well as goodness of fit diagnostics
Other scripts are functions to be sourced while running the analysis.
- Clara CHAMPAGNE - @GitHub - [email protected]
This readme has been built with Bilal BENHANA thanks to a template