Andolina2022

This repository includes the R code and data used in the analysis for the main manuscript of the paper. The cleaned data file consists of the data for only the 104 incident infections used. The ped.RDS file is an R data file for the piece-wise exponential data formulation of the survival data for the competing risks analysis. The descriptives file consists of all descriptive analyses conducted in the study whether included or not. The gametocyte incidence file consists of the R code for the competing risks analysis for gametocyte incidence and malaria clearance. The Clearance Kaplan-Meier is the file used to capture the Kaplan-Meier of the time to clearance of parasites (Table 2). The parasite density, gametocyte density, gametocyte fraction file are the R codes for the longitudinal non-linear mixed effects models (Table 2) and should be executed in that order. The "sensitivity analysis intervals.R" file includes the R code used for the sennsitivity surrounding the interval-censoring nature of the data. The sensitivity analysis zipped folder contains the R code for the sensitivity analysis when we include only infections that are never symptomatic (folder - only ever symptomatic) or infections that have an initial parasite density above 0.1 (folder - cutoff parasite density).