Hello.
I am trying to write an R function to plot the survival function (and
associated hazard and density) for a Siler competing hazards model.
This model is similar to the Gompertz-Makeham, with the addition of a
juvenile component that includes two parameters---one that describes
the initial infant mortality rate, and a negative exponential that
describes typical mortality decline over the juvenile period. The
entire hazard is expressed as
h(x) = a1*exp(-b1*x)+a2+a3*exp(b3*x)
I've had success in plotting the curves using the following function:
############################################################
siler<-function(x=c(0.1,0.5,0.001,0.003,0.05)) # model Siler parameters
{
sil=function(t)
{
a1 = x[1]
b1 = x[2]
a2 = x[3]
a3 = x[4]
b3 = x[5]
h.t<-a1*exp(-b1*t)+a2+a3*exp(b3*t)
S.t<-exp(-a1/b1*(1-exp(-b1*t))-a2*t+a3/b3*(1-exp(b3*t)))
d.t<-S.t*h.t
#return(d.t)
return(S.t) # returns the survival function
#return(h.t)
}
t=seq(0,100,0.01)
plot(t,sil(t),ylim=c(0,1),type='l',main="Siler model of mortality:
Wood et al. (2002, Figure
7.4)",cex.main=0.9,cex.lab=0.8,cex.axis=0.75,ylab='S(t)',xlab='Age
(years)') # reproduces Figure 7.4 from Wood et al. (2002)
}
siler()
#########################################################################
How can I modify the function so that I can plot curves using
published Siler parameters I have already compiled into a dataframe
(below)?
names<-c("Hadza","Ache")
a1<-c(0.351,0.157)
b1<-c(0.895,0.721)
a2<-c(0.011,0.013)
a3<-c(0.0000067,0.000048)
b3<-c(0.125,0.103)
sil.anthro<-data.frame(cbind(names,a1,b1,a2,a3,b3))
For example, how can I modify the function above to produce a curve
for the a specific group (e.g., Hadza, Ache...) or multiple groups on
one graph? Thanks.
--Trey
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