Registered adolescent homicide mortality in Colombia, 2015–2024: data and reproducibility package
Description
Version 3 of this repository provides the processed analytic data, R code, model outputs, diagnostic files, supplementary tables, figure source data, and reproducibility documentation supporting the study “Registered adolescent homicide mortality in Colombia, 2015–2024: Bayesian spatiotemporal mapping of geographic inequality.” The study examined registered homicide mortality among adolescents aged 10–19 years in Colombia from 2015 to 2024 using Bayesian areal disease-mapping models with BYM2 spatial effects, random-walk temporal components, and candidate space–time interaction structures. The repository includes aggregated department–year–sex–age data, population denominators, department-level Multidimensional Poverty Index covariates, spatial boundary and adjacency files, posterior annual and department-level mortality estimates, exceedance probabilities, hotspot-persistence metrics, formal spatial-inequality measures, MPI-adjusted residual spatial-risk estimates, model-comparison outputs, calibration diagnostics, and sparse-count and likelihood-sensitivity analyses. Version 3 additionally includes posterior-predictive and calibration assessments, hyperprior sensitivity analyses, MPI measurement-precision and measurement-error sensitivity analyses, spatial-graph and leave-archipelago influence analyses, regenerated supplementary tables, and source files for the main and supplementary figures. Data dictionaries, file manifests, checksums, execution guidance, citation information, and licensing documentation are included to support transparent reproduction of the analytic workflow, tables, figures, and numerical results. Record-level medico-legal data and other source microdata are not redistributed. The deposited files consist of aggregated, processed, or derived materials suitable for public sharing and are intended to support verification and reproduction of the reported results.
Files
Steps to reproduce
Download and extract all repository files while preserving the directory structure. Set the R working directory to the repository root. Detailed software requirements, package versions, file dependencies, and execution guidance are provided in `REPRODUCIBILITY.md` and `00_documentation/execution_order.md`. To reproduce the deposited supplementary tables and figures from the archived analytic outputs, run `02_code/tables/11_generate_supplementary_tables.R`, followed by the figure scripts in numerical order: `02_code/figures/12_Figure1_Homicide_Main_ABC_.R` `02_code/figures/13_Figure2_Homicide_SexAge_Hotspots.R` `02_code/figures/14_Figure3_Homicide_ResidualRisk.R` `02_code/figures/15_FigureS1_Homicide_rPIT.R` To reproduce the model-derived estimates and all diagnostic and sensitivity analyses from the deposited processed analytic data, execute the following scripts in order: `02_code/modeling/04_fit_bayesian_spatiotemporal_models.R` `02_code/modeling/05_derive_posterior_metrics.R` `02_code/sensitivity_analysis/06_assess_hyperprior_sensitivity.R` `02_code/sensitivity_analysis/06b_assess_mpi_measurement_precision.R` `02_code/sensitivity_analysis/06c_assess_mpi_measurement_error.R` `02_code/sensitivity_analysis/07_assess_zero_count_structure.R` `02_code/sensitivity_analysis/08_assess_sparse_strata_likelihoods.R` `02_code/sensitivity_analysis/09_run_posterior_predictive_zero_checks.R` `02_code/sensitivity_analysis/09b_run_posterior_predictive_count_checks.R` `02_code/sensitivity_analysis/10_assess_insular_graph_connectivity.R` `02_code/sensitivity_analysis/10b_assess_archipelago_influence.R` `02_code/tables/11_generate_supplementary_tables.R` The Bayesian models were fitted using R 4.6.0 and R-INLA 26.6.8. Expected outputs are written to `03_model_outputs/`, `04_diagnostics_and_sensitivity/`, `05_tables/`, `06_figures/`, and `07_audit_records/`. Regenerated outputs may be compared with the deposited supplementary tables, figure source data, model summaries, posterior-derived metrics, diagnostics, manifests, and checksums. The scripts in `02_code/data_preparation/` document the upstream construction of population denominators, MPI covariates, the analytic panel, and the spatial graph. Complete reconstruction of those upstream inputs from original source records may require access to third-party data that are not redistributed. The deposited repository provides the aggregated analytic data and derived outputs necessary to reproduce the reported model-based estimates, tables, figures, diagnostics, and documented analytic workflow.
Institutions
- Pontificia Universidad Católica del EcuadorPichincha, Quito