options(digits=3)
png(filename="probe_match-%02d.png",res=100)
library(pomp2)
gompertz() -> po
po %>% as.data.frame() %>% subset(select=-X) -> dat
plist <- list(
mean=probe.mean("Y",trim=0.1,transform=sqrt),
sd=probe.sd("Y",transform=sqrt),
probe.marginal("Y",ref=obs(po)),
probe.acf("Y",lags=c(1,3,5),type="correlation",transform=sqrt),
probe.quantile("Y",prob=c(0.25,0.75),na.rm=TRUE)
)
try(dat %>% probe_objfun())
try(dat %>% probe_objfun(times="time",t0=0))
dat %>%
probe_objfun(
times="time",t0=0,
rinit=po@rinit,
rprocess=po@rprocess,
rmeasure=po@rmeasure,
probes=plist,
params=coef(po),
nsim=100,
seed=5069977
) -> f
stopifnot(f(0)==f(1))
f %>% probe_objfun(est=c("K"),seed=580656309) -> f1
plot(sapply(seq(0.8,1.6,by=0.1),f1))
f1(1.1)
library(subplex)
subplex(fn=f1,par=0.4,control=list(reltol=1e-3)) -> out
f1(out$par)
try(probe_objfun())
try(probe_objfun("bob"))
try(probe_objfun(f,est="harry"))
f1 %>% as("probed_pomp") %>% plot()
f1 %>% summary() %>% names()
f1 %>% probe() %>% plot()
f1 %>% as.pomp() %>% as.data.frame() %>% names()
f1 %>% probe_objfun(fail.value=1e10) -> f2
f1 %>% spect(kernel.width=3,nsim=100,seed=748682047) %>% plot()
f1 %>% as("pomp")
f1 %>% as("data.frame") %>% names()
po %>% probe_objfun(nsim=100,probes=function(x)1,fail.value=1e9) -> f2
logLik(f2)
f2(1)
dev.off()
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