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Appendix 
This appendix provides R code with annotations for fit- 
ting data (by using maximum likelihood) to a multiple- 
stage transition model with 3 stages. The code can be 
expanded by adding more stages. The procedure re- 
quires that data to be in a data frame called “Stg” that 
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417:159-170. 
consists of at least 2 vectors, one called “stage,” which 
contains the stage for each sample, and one called 
“time,” containing the time at which each sample was 
measured. Annotations are in italics. 
library! stats4) #The statsd library contains the required mle function 
Stage=function(T50_l,T50_2,sl,s2){ #this function calculates the negative log likelihood 
#given the data and a set of parameters. Additional stages 
thvould require further parameters to be included here. 
ave=l+(l/(l+(Stg$Time/T50_l) A sl))+ #“ave” is the average stage at each time 
