Simulation of illness-death model

Usage

simMultistate(
  n,
  cumhaz,
  cumhaz2,
  death.cumhaz,
  death.cumhaz2,
  rr = NULL,
  rr2 = NULL,
  rd = NULL,
  rd2 = NULL,
  gap.time = FALSE,
  max.recurrent = 100,
  dependence = 0,
  var.z = 0.22,
  cor.mat = NULL,
  cens = NULL,
  ...
)

Arguments

n: number of id's
cumhaz: cumulative hazard of going from state 1 to 2.
cumhaz2: cumulative hazard of going from state 2 to 1.
death.cumhaz: cumulative hazard of death from state 1.
death.cumhaz2: cumulative hazard of death from state 2.
rr: relative risk adjustment for cumhaz
rr2: relative risk adjustment for cumhaz2
rd: relative risk adjustment for death.cumhaz
rd2: relative risk adjustment for death.cumhaz2
gap.time: if true simulates gap-times with specified cumulative hazard
max.recurrent: limits number recurrent events to 100
dependence: 0:independence; 1:all share same random effect with variance var.z; 2:random effect exp(normal) with correlation structure from cor.mat; 3:additive gamma distributed random effects, z1= (z11+ z12)/2 such that mean is 1 , z2= (z11^cor.mat(1,2)+ z13)/2, z3= (z12^(cor.mat(2,3)+z13^cor.mat(1,3))/2, with z11 z12 z13 are gamma with mean and variance 1 , first random effect is z1 and for N1 second random effect is z2 and for N2 third random effect is for death
var.z: variance of random effects
cor.mat: correlation matrix for var.z variance of random effects
cens: rate of censoring exponential distribution
...: Additional arguments to lower level funtions

Details

simMultistate with different death intensities from states 1 and 2

Must give cumulative hazards on some time-range

Author

Thomas Scheike

Examples

########################################
## getting some rates to mimick 
########################################
data(CPH_HPN_CRBSI)
dr <- CPH_HPN_CRBSI$terminal
base1 <- CPH_HPN_CRBSI$crbsi 
base4 <- CPH_HPN_CRBSI$mechanical
dr2 <- scalecumhaz(dr,1.5)
cens <- rbind(c(0,0),c(2000,0.5),c(5110,3))

iddata <- simMultistate(1000,base1,base1,dr,dr2,cens=cens)
dlist(iddata,.~id|id<3,n=0)
#> id: 1
#>      time status entry death from to start    stop
#> 1 295.152      3     0     1    1  3     0 295.152
#> ------------------------------------------------------------ 
#> id: 2
#>       time status entry death from to start     stop
#> 2 296.3073      3     0     1    1  3     0 296.3073
 
### estimating rates from simulated data  
c0 <- phreg(Surv(start,stop,status==0)~+1,iddata)
c3 <- phreg(Surv(start,stop,status==3)~+strata(from),iddata)
c1 <- phreg(Surv(start,stop,status==1)~+1,subset(iddata,from==2))
c2 <- phreg(Surv(start,stop,status==2)~+1,subset(iddata,from==1))
###
par(mfrow=c(2,3))
bplot(c0)
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
lines(cens,col=2) 
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
bplot(c3,main="rates 1-> 3 , 2->3")
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
lines(dr,col=1,lwd=2)
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
lines(dr2,col=2,lwd=2)
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
###
bplot(c1,main="rate 1->2")
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
lines(base1,lwd=2)
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
###
bplot(c2,main="rate 2->1")
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet
lines(base1,lwd=2)
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet