An individual-based modelling study estimating the impact of maternity service delivery on health in Malawi - Code and data repository

This is a release of the Thanzi La Onse model (tlomodel.org) code specifically for the analysis conducted in the paper "An individual-based modelling study estimating the impact of maternity service delivery on health in Malawi". In addition, the unprocessed logfiles for the analysis conducted in this paper are available here.   Please note, due to Zenodos restriction on file sizes, we include the model code and unprocessed data over two versions of this Zenodo entry (Versions 2 and 3 of this entry).  Version 3 (this version) includes the full model code whilst version 2 includes the unprocessed data.   The folder ‘Source code – The TLO model.zip’ is the compressed source-code of the model and includes the entire model code, the relevant scenario files (files used to run the model and enact changes in each scenario defined in the manuscript) and analysis files (used to output model results and figures using .log files generated by scenario files). Whilst the entire model is used to generate the results presented in this paper, the following files compromise the maternal and newborn health model and can be found within the folder as: TLOmodel/src/tlo/methods/care_of_women_during_pregnancy.py TLOmodel/src/tlo/methods/pregnancy_supervisor.py TLOmodel/src/tlo/methods/labour.py TLOmodel/src/tlo/methods/postnatal_supervisor.py TLOmodel/src/tlo/methods/newborn_outcomes.py The individual python scripts can be reviewed by downloading and unzipping the file and opening a script in any .txt editor. Alternatively, to use this compressed file to install and run the model on a local machine: Download ‘Source code – The TLO model.zip’ from Zenodo and unzip the folder Follow the model installation instructions found here -tlomodel.org Line 1 of the command line code should point to your local version of the code Use the command ‘tlo scenario-run’ followed by the local path for any of the scenario files to run the model   The file ‘Raw data.zip’ (Version 2 of this entry) contains the unprocessed .log files outputted from each scenario file and analysed to produce the results in this manuscript. Within this folder there is a README file detailing the names of each scenario files as it relates to the named scenarios in the manuscript (e.g. Status Quo). All scenario files can be reviewed by downloading ‘Source code – The TLO model.zip’ and accessing TLOmodel/src/scripts/maternal_perinatal_analyses/scenario_files   Finally, the scripts used to analyse the .log files and produce results can be ran locally and are found at: (Figures 1, S33-S79) TLOmodel/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py (Figures 2, 3, 4, S80-S85) TLOmodel/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py   If you encounter any issues installing and/or running the code, please contact joseph.h.collins@ucl.ac.uk.