tambe-elvis/cameroon_polio_inequity_reproducibility

Reproducibility package for the analysis of immunization inequity trends and ecological concordance with vaccine-derived poliovirus detections in Cameroon. # Cameroon Immunization Inequity and cVDPV Concordance — Reproducibility Package **Study title:** Immunization inequity trends and ecological concordance with vaccine-derived poliovirus detections in Cameroon: 1998 to 2018 survey and 2015 to 2024 surveillance analysis **Manuscript ID:** PONE-D-26-25926 (PLOS ONE) **Author:** Tambe Elvis Akem **Package version:** 1.2 Version 1.2 is a reproducibility/provenance cleanup only. No scientific values, manuscript tables, or analytical results were changed. The update externalises the national surveillance values into a bundled source-aligned CSV, aligns master-workbook labels with the revised manuscript terminology (WUENIC, DTP1-DTP3 percentage-point difference, and FCS periods), corrects the WHO POLIS reference number for unattributed cVDPV counts, and fixes installation/documentation wording. --- ## What this package does Running `python run_all.py` reproduces every table and figure in the manuscript from the bundled analytical inputs. Survey-derived results are regenerated from the Cameroon WHO HEAT extract; the national programme/surveillance panel is regenerated from a source-aligned WUENIC/POLIS input file: - **Tables 1-4** (national survey trends, wealth-based inequality with fixed Q1/Q5 endpoints, 2018 multidimensional inequality, national surveillance panel) - **Supplementary tables S2-S5** (geographic harmonization/concordance, survey-derived subgroup estimates with 95% confidence intervals, standard concentration index vs. ECCI, and four prespecified sensitivity analyses) - **Figures 1-3** (national coverage trends, wealth-related inequality, Pol3/IPV/cVDPV surveillance), each exported as PNG (200 DPI, manuscript preview) and TIFF (600 DPI, LZW compression, publication-quality submission) No manuscript figure is hand-edited after generation; every pixel comes from this pipeline. --- ## Software requirements - Python >= 3.12 is required. See `requirements.txt` for minimum pip package versions (or `env …