Comments (2)
commented on July 17, 2024
Furthermore, former when I used the following parameterization, it works
sir<-pomp(data=data.frame(cases=data,time=seq(1,14,by=1)),
times="time",t0=0,
dmeasure=Csnippet(dmeas),
rmeasure=Csnippet(rmeas),
rprocess=euler.sim(
step.fun=Csnippet(sir.step),delta.t=1/14/2),
statenames=c("S","I","R"),
paramnames=c("popsize","bet","mu","rho","S.0","I.0","R.0","theta"),
initializer=function(params,t0,...){
fracs<-params[c("S.0","I.0","R.0")]
return(setNames(c(round(params["popsize"]*fracs/sum(fracs))),c("S","I","R")))
setNames(c(round(params["popsize"]*fracs/sum(fracs))),c("S","I","R"))
},
params=c(popsize=763,theta=100,bet=2,mu=0.5,rho=3,S.0=757,I.0=3,R.0=3))
however, after I changed the parameterization to above, it doesn't work. Where is the problem?
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kingaa
commented on July 17, 2024
The error message tells me that initializer is supposed to return a named numeric vector. Does it?
sir <- pomp(data=data.frame(cases=NA,time=seq(1,14,by=1)),
times="time",t0=0,dmeasure=Csnippet(dmeas),
rmeasure=Csnippet(rmeas),
rprocess=euler.sim(
step.fun=Csnippet(sir.step),delta.t=1/14/2),
statenames=c("S","I","R"),
paramnames=c("popsize","bet","mu","rho","theta1","theta2","theta"),
initializer=function(params,t0,...){
ps<-exp(params["theta1"])/(1+exp(params["theta1"])+exp(params["theta2"]))
pi<-1/(1+exp(params["theta1"])+exp(params["theta2"]))
pr<-exp(params["theta2"])/(1+exp(params["theta1"])+exp(params["theta2"]))
x <- setNames(rmultinom(1,params["popsize"],prob=c(ps,pi,pr)),
c("S","I","R"))
print(class(x))
x
},
params=c(popsize=763,theta=100,bet=2,mu=0.5,rho=3,theta1=5,theta2=1)
)
sir<-simulate(sir,seed = 73691676L)
Which gives:
[1] "matrix"
Error: in ‘simulate’: in 'init.state': user 'initializer' must return a named numeric vector
So, it appears that rmultinom returns a matrix, not a vector. See ?rmultinom to confirm this. If I do instead
sir <- pomp(data=data.frame(cases=NA,time=seq(1,14,by=1)),
times="time",t0=0,
dmeasure=Csnippet(dmeas),
rmeasure=Csnippet(rmeas),
rprocess=euler.sim(
step.fun=Csnippet(sir.step),delta.t=1/14/2),
statenames=c("S","I","R"),
paramnames=c("popsize","bet","mu","rho","theta1","theta2","theta"),
initializer=function(params,t0,...){
ps<-exp(params["theta1"])/(1+exp(params["theta1"])+exp(params["theta2"]))
pi<-1/(1+exp(params["theta1"])+exp(params["theta2"]))
pr<-exp(params["theta2"])/(1+exp(params["theta1"])+exp(params["theta2"]))
setNames(as.numeric(
rmultinom(1,params["popsize"],prob=c(ps,pi,pr))),
c("S","I","R"))
},
params=c(popsize=763,theta=100,bet=2,mu=0.5,rho=3,theta1=5,theta2=1)
)
sir<-simulate(sir,seed = 73691676L)
all is well.
In your second snippet of code above, note that your second setNames(...) call goes unevaluated due to the previous return call. Also note that this returns a named numeric vector, hence the success where the previous codes failed.
Hope this helps.
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