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ki-longitudinal-growth

This repository includes scripts to replicate the analyses included in the UC Berkeley team's analysis of wasting and stunting as part of the Bill and Melinda Gates Foundation's KI project.

Directory structure

0-project-functions : internal functions used in analysis and figure generation

1-data-cleaning : scripts to prepare data for analysis

2-descriptive outcomes : analysis scripts

3-prep-tmle-analysis : scripts to prepare data for tmle

`4-longbow-tmle-analysis : scripts to run TMLE analysis on the Longbow platform (within the "run-longbow" subfolder) as well as scripts to compile and pool results

5-visualizations : scripts that produce figures

  • risk factors

    • fig-rf-study-inventory-heatmap.R corresponds to C+C manuscript Fig 1
    • fig-Zscore-PAR-plots.R corresponds to C+C manuscript Fig 2
    • fig-PAR-VIM-comparison.R corresponds to C+C manuscript Fig 2 inset
    • fig-age-strat-rf-comp.R corresponds to C+C manuscript Fig 3b
    • fig-wast-perswast-comp.R corresponds to C+C manuscript Fig 3c
    • fig-spline-plots.R corresponds to C+C manuscript Fig 3a
    • fig-early-wast.R corresponds to C+C manuscript Fig 4b
    • fig-wlz-quart-laz-velocity.R corresponds to C+C manuscript Fig 4a
    • fig-mortality-plots.R corresponds to C+C manuscript Fig 4c
    • rf_manuscript_figure_grids.R compiles figures into manuscript grids
    • Extended data figures
      • fig-example-forest.R corresponds to C+C manuscript Extended Fig 1
      • fig-sig-heatmap.R corresponds to C+C manuscript Extended Fig 2
      • fig-Zscore-PAR-extended-data-plots.R corresponds to C+C manuscript Extended Fig 3,4,7,8
      • fig-PAF-plots.R corresponds to C+C manuscript Extended Fig 5
      • fig-mediation-analysis.R corresponds to C+C manuscript Extended Fig 6
      • fig-wlz-quart-stunting.R corresponds to C+C manuscript Extended Fig 9
      • fig-mortality-timing.R corresponds to C+C manuscript Extended Fig 10
      • fig-adjustment-effect-by-cov-number.R corresponds to C+C manuscript Extended Fig 11
      • fig-EValues.R corresponds to C+C manuscript Extended Fig 12
    • Supplimental figures - used in online supplimentary information
    • fig-kaplan-meier-curves.R
    • fig-Zscore-PAR-extended-data-plots-FE.R
      • fig.RR-plots.R
    • fig-spline-plots_sensitivity.R
    • fig-sig-heatmap-FE.R
    • fig-pooled.RR-plots.R
    • fig-muac-mort.R
    • fig-mortality-plots-sens-birth.R
    • fig-mortality-plots-sens.R
    • fig-mortality-plots-sens2.R
    • fig-mortality-plots-sens3.R
    • fig-muac-mort.R

  • shared

    • fig-CONSORT-figure1 corresponds to stunting and wasting manuscripts Extended Fig 1

  • stunting

    • fig-DHS-plots-laz.R: corresponds to stunting manuscript Fig 2
    • fig-study-inventory-heatmaps-stunt.R: corresponds to stunting manuscript Fig 1
    • fig-stunting-descriptive-epi-plots.R: corresponds to stunting manuscript Fig 3 (includes other figures as well, some of which are not included in the manuscript currently)
    • fig-stunting-descriptive-epi-plot-monthly24.R: sensitivity analysis for Fig 3 that subsets cohorts to those with monthly measurements each month from 0 to 24 months
    • fig-stunting-flow.R: corresponds to stunting manuscript Fig 4a
    • fig-stunting-length-velocity.R: corresponds to stunting manuscript Fig 5
    • fig-stunting-length-velocity-subset.R: sensitivity analysis for Fig 5 that excludes COHORTS Guatemala and Content cohorts
    • fig-stunting-prevalence-map.R: corresponds to stunting manuscript Extended Data Fig 2
    • fig-stunting-rec-density.R: corresponds to stunting manuscript Fig 4b
    • fig-stunting-rec-prev.R: corresponds to stunting manuscript Fig 4c

  • wasting

    • fig-wasting-study-inventory-heatmap.R corresponds to wasting manuscript Fig 1
    • fig-wasting-descriptive-epi-plots.R corresponds to wasting manuscript Fig 2a-c, Fig4b,d, and Fig5a (includes many other figures as well, some of which are not included in the manuscript currently)
    • fig-wasting-classification-example.R corresponds to wasting manuscript Fig 4a
    • fig-wasting-rec-hist.R corresponds to wasting manuscript Fig 4c
    • fig-wasting-seasonality.R corresponds to wasting manuscript Fig 3a-c
    • fig-wasting-seasonality-diff-plot.R corresponds to wasting manuscript Fig 3d
    • fig-wasting-birth-traj.R corresponds to wasting manuscript Fig 4e
    • fig-birth-wasting-recovery-stats.R corresponds to wasting manuscript Fig 4e inset
    • fig-wasting-prevalence-map.R corresponds to wasting manuscript Extended Fig 2
    • fig-DHS-plots-zscores.R corresponds to wasting manuscript Extended Fig 3
    • fig-pers-wasting.R corresponds to wasting manuscript Extended Fig 4a
    • fig-co-flow.R corresponds to wasting manuscript Fig 5b
    • fig-co-initial-onset.R in progress: creates plot of initial onset of wasting and stunting in children with both
    • fig-wasting-traj.R archived; not used

data : folder containing datasets that live off secure remote data server (agregate results or external data, but no subject-level data)

figures : folder containing figure outputs from scripts from 5-visualizations

results : folder containing output from analyses that do not contain identifiers