neotree/small-vulnerable-newborns

Analysis code for the study of small vulnerable newborn (SVN) outcomes across two tertiary neonatal units in Malawi and Zimbabwe (Neotree, Kamuzu Central Hospital and Sally Mugabe Central Hospital, 2022-2025). Includes a run_all.R script to reproduce every table and figure from the data (not included — see input/README.md). # small-vulnerable-newborns Analysis code for the study **"Small vulnerable newborn outcomes across Malawi and Zimbabwe: secondary analysis of a prospective neonatal cohort"** (Neotree, Kamuzu Central Hospital and Sally Mugabe Central Hospital, 2022-2025). This repository contains the complete R analysis pipeline so that every table and figure in the manuscript is reproducible. The underlying clinical data are confidential and are **not** included — see DATA_AVAILABILITY.md. ## What the study does Compares the INTERGROWTH-21st small-vulnerable-newborn (SVN) framework (Term-AGA, Term-SGA, Preterm-AGA, Preterm-SGA) against birth-weight-alone (low birth weight, LBW) classification for describing outcomes among live births and neonatal-unit admissions, examines independent predictors of neonatal death (univariable and multivariable), and tests whether SVN classification derived from routinely estimated gestational age holds up when validated against an ultrasound-dated subset. ## Repository layout ``` scripts/ All R analysis and figure scripts input/ Confidential data goes here (not committed) -- see input/README.md output/ Pipeline outputs land here (not committed) run_all.R Runs the whole pipeline end to end FIGURE_TABLE_SOURCES.md Map of each manuscript table/figure -> source script DATA_AVAILABILITY.md Data/code availability statement and access terms ``` ## Pipeline - Every script sources `scripts/00a_setup_shared.R`, which defines the INTERGROWTH-21st SGA lookup, SVN classification, plausible-range outlier handling, colour palettes, plotting theme, and the six data-file paths (all resolved relative to the script's own location, so the repo can be cloned anywhere). - Most scripts read only the raw `input/` data. A small number of `Figure_*`/`helper_*` scripts read a CSV written by an earlier `Table_*`/`dep_*` script in the same run — `run_all.R` runs everything in the correct order …