This is the code used to for the analyses in the manuscript "Estimating the optimal CD4 count for HIV-infected persons to start antiretroviral therapy." No data files are included.

  • Main.nw: Main.nw is a Sweave file that serves as the central program to prep the data for analysis, compute the regimen rules, call the appropriate functions to perform the analysis (see below for an explanation of each function), and then format the results in tables and graphs. Data necessary for the analysis are in four separate files -- the clinic data including CD4 and viral load information (d2), non-ADE information for each subject (non.ade), the treatment data containing one record per treatment for a given subject (trt), and the ADE or OI information for each subject (oi.df) with a given subject potentially having up to 4 ADEs listed for a given age.

  • solution.R: R function that merges the clinic and treatment data accounting for any gaps in treatment.

  • build.time.df6.R: R function that creates the time-dependent data frame based on the months of follow-up. Follow-up of 6, 12, 24, and 36 months were considered. These data were used when calculating weights.

  • R function that computes the utilities, fits models used to compute the inverse-probability weights, and estimates the CD4 at which each utility is maximized.

  • bootstrap6.R: R function that calculates the bootstrapped confidence intervals if the logical "bootstrap" is set to TRUE. It performs nboot number of replications.

  • regRule.R: R function that assigns regimens based on pre-specified rules regarding CD4 counts.

Topic revision: r12 - 21 Sep 2011, BryanShepherd

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