laurabalzer / search_analysis_adults

R code for evaluating adult HIV incidence, health, & implementation outcomes for the first phase of the SEARCH Study (https://www.searchendaids.com/). Full statistical analysis plan available at https://arxiv.org/abs/1808.03231

This repository contains the functions to implement the Two-Stage analysis for estimating the effect of the SEARCH intervention on adult outcomes. The SEARCH statistical analysis plan is available at https://arxiv.org/abs/1808.03231.

R Code by Laura B. Balzer, Yea-Hung Chen, and Joshua Schwab

Stage 1: Estimate the community-level outcome.

• Cumulative HIV incidence: HIV_Master.R, HIV_Functions.R

• NCD analyses: NCD_Master.R, NCD_Functions.R

• Population-level viral suppression & UNAIDS 90/90/90: Cascade_Master.R, Cascade_Functions.R

• Suppression and ART start among closed cohort: SuppressionInClosedCohort.R

• Annual HIV incidence in the intervention arm: Estimate Incidence.R

• Cumulative HIV testing: Cumulative Testing.R

• Mortality: mortality analysis.r

• Tuberculosis analyses: tuberculosis analysis.r

Stage 2: Estimate the intervention effect, given community-level covariates, exposure, and outcomes.

• Stage2_Functions.R
• Adapt_Functions.R

Also includes code for descriptive analyses described in the statistical analysis plan:

• baseline chars.R
• baseline prev by age and sex and region.R
• patient flow primary endpoint.Rmd
• Open Cohort Patient Flow.R
• Annual HIV Incidence Cohorts in Intervention Arm.Rmd
• changes in Circumcision.Rmd

Helper functions used in analyses for HIV incidence, NCD, suppression/coverage:

• Stage1_Functions

Helper functions used in mortality/tuberculosis analyses:

• impute dates.r
• define survival variables.r
• community-level estimates.r
• Preprocess_Functions.R
• s2.r

Helper functions used in analyses for cumulative testing, suppression/ART in the closed cohort, estimating annual incidence in the intervention arm

• Utils.R