Analysis.R for How uncertain is the survival extrapolation? A study of the impact of different parametric survival models on extrapolated uncertainty about hazard functions, lifetime mean survival and cost-effectiveness

Code used to analyse the dataset "Data.Rda" provided in this project. Produces extrapolations, estimates of lifetime mean survival and a hypothetical cost-effectiveness analysis. These are summarised via figures and tables, as presented in the manuscript "How uncertain is the survival extrapolation? A study of the impact of different parametric survival models on extrapolated uncertainty about hazard functions, lifetime mean survival and cost-effectiveness."<div><br></div><div>To use this code, the libraries loaded at the start of the script need to be pre-installed, and Data.Rda should be placed in the same folder as this script.</div><div><br></div><div>To visualise the hazard function, the functions 'pehaz' and 'muhaz' are used from the 'muhaz' library, giving noisy (piece-wise) and smooth estimates, respectively. Uncertainty about these estimates is obtained via bootstrapping.</div><div><br></div><div>The package 'flexsurv' is used to fit seven standard parametric survival models (exponential, Weibull, Gompertz, Gamma, log-normal, loglogistic and generalised gamma).</div><div><br></div><div>Also included is code for a simple two-state (well-death) markov model and corresponding health economic evaluation (cost-effectiveness analysis). Probabilistic sensitivity analysis (PSA) is carried out - this uses 10,000 samples. Only uncertainty in the survival models is considered. To output the results of this PSA it is assumed that a folder exists called 'SAVI' - data are exported into this folder, ready for analysis at <a href="http://savi.shef.ac.uk/SAVI/">http://savi.shef.ac.uk/SAVI/</a> (note the results of this further analysis are not reported as most value of information estimates were zero).</div><div><br></div><div><br></div><div><br></div>