On Jun 28, 2011, at 6:26 PM, David Winsemius wrote:
On Jun 28, 2011, at 5:46 PM, Trey Batey wrote:
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:
I modified your function to have named parameters:
############################################################
siler<-function(a1=0.1, b1=0.5,a2=0.001,a3=0.003,b3=0.05) # model
Siler parameters
{
sil=function(t)
{ 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)
cbind outputs a matrix and the presence of character values means
all your numbers are now character.... bad programming practice. Fix
is here:
> sil.anthro[, 2:6] <- sapply(sil.anthro[, 2:6], function(x)
as.numeric(as.character(x)) )
> str(sil.anthro)
'data.frame': 2 obs. of 6 variables:
$ names: Factor w/ 2 levels "Ache","Hadza": 2 1
$ a1 : num 0.351 0.157
$ b1 : num 0.895 0.721
$ a2 : num 0.011 0.013
$ a3 : num 6.7e-06 4.8e-05
$ b3 : num 0.125 0.103
> with( sil.anthro[1, -1], siler(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3) )
> with( sil.anthro[2, -1], siler(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3) )
Seems to work.
--
David.
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.
Could use names as index
with( sil.anthro[sil.anthro$names=="Hadza", ],
siler(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3) )
And maybe even clearer would be:
> row.names(sil.anthro) <- sil.anthro$names
> with( sil.anthro["Hadza", ], siler(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3) )
You probably should have done that originally as:
sil.anthro<-data.frame(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3)
row.names(sil.anthro) <- names
(But even better woulbe to choose a 'name' other than 'names'.)
--
David Winsemius, MD
West Hartford, CT
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David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
