Saturday, December 21, 2013

Use simulated Gompertz random number to test flexsurv Gompertz and Weibull fitting results

Summary: I experimented the sample size. For 50 cells, the Gompertz model may be the better fit 4 out of 5 times. For 100 cells, Gompertz is better than Weibull maybe 9 out of 10 times. For 500 cells, Gompertz is always bettern than the Weibull model.

Conclusion: For most yeast life span assay, it is not always easy to tell whether Gompertz or Weibull is a better fit.

Comments: The actual results probably also depend on R and G, which determine the variance.

code: 20131221.gompertz.simulation.R

# generate gompertz random numbers
# fit with flexsurv Gompertz and weibull models

#inverse of gompertz CDF
# see
inverse.gomp.CDF = function(R,G,y) {  (1/G)*log(1 - (G/R)*log(1-y)  ) }

#see generate random number with a given distribution

x.uniform = runif(60)

x.gompertz = inverse.gomp.CDF(0.001,0.2, x.uniform)


tb = calculate.s(x.gompertz)
plot(tb$s ~ tb$t)

lifespan = x.gompertz
lifespanGomp = flexsurvreg(formula = Surv(lifespan) ~ 1, dist = 'gompertz')  
lifespanWeib = flexsurvreg(formula = Surv(lifespan) ~ 1, dist = 'weibull')  

c(lifespanWeib$AIC, lifespanGomp$AIC, lifespanWeib$AIC - lifespanGomp$AIC )

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