Nothing
## NOT RUN: won't work on CRAN
## FIXME: set up environment variables to allow this to run
## if not on CRAN
library("R2admb")
tadpoledat <-
data.frame(TBL = rep(c(9,12,21,25,37),each=3),
Kill = c(0,2,1,3,4,5,0,0,0,0,1,0,0,0,0L),
nexposed=rep(10,15))
if (FALSE) {
setup_admb()
file.copy(system.file("tplfiles",
"ReedfrogSizepred0.tpl",package="R2admb"),
"tadpole.tpl")
m1 <- do_admb("tadpole",
data=c(list(nobs=15),tadpoledat),
params=list(c=0.45,d=13,g=1),
bounds=list(c=c(0,1),d=c(0,50),g=c(-1,25)),
run.opts=run.control(checkparam="write",
checkdata="write",clean=FALSE))
unlink("tadpole.tpl")
summary(m1)
read.table("tadpole_gen.std",header=TRUE)[,4]
sqrt(diag(read_admb("tadpole_gen")$vcov))
sqrt(diag(read_pars("tadpole_gen")$vcov))
## compare with mle2 results:
## library("bbmle")
## m2 <- mle2(Kill~dbinom(prob=c*(TBL/d*exp(1-TBL/d))^g,size=nexposed),
## data=tadpoledat,
## start=as.list(coef(m1)))
m2_vcov <- structure(c(0.0158042534788236,
0.0578065701530253, 0.504366729952002,
0.0578065701530253, 0.657825248678555,
2.24662255486992, 0.504366729952002,
2.24662255486992, 36.3935910094069),
.Dim = c(3L, 3L), .Dimnames = list(
c("c", "d", "g"),
c("c", "d", "g")))
all.equal(vcov(m1),m2_vcov,tol=2e-4)
}
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