Nothing
library(R2admb)
s <- try(setup_admb())
if (!identical(aa <- admb_version(),NA)) {
## run only if we can
file.copy(system.file("tplfiles","ReedfrogSizepred0.tpl",package="R2admb"),"tadpole.tpl")
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))
par1 <- list(c=0.45,d=13,g=1)
## getvals(par1,"value",valsOK=TRUE)
m1 <- do_admb("tadpole",
data=c(list(nobs=15),tadpoledat),
params=par1,
bounds=list(c=c(0,1),d=c(0,50),g=c(-1,25)),
run.opts=run.control(checkparam="write",
checkdata="write",clean="all"))
m1P <- do_admb("tadpole",
data=c(list(nobs=15),tadpoledat),
params=par1,
bounds=list(c=c(0,1),d=c(0,50),g=c(-1,25)),
phase=list(c=1,d=2,g=-1),
run.opts=run.control(checkparam="write",
checkdata="write",clean="all"))
par2 <- list(c=list(0.45,bounds=c(0,1)),
d=list(13,bounds=c(0,50)),
g=list(1,bounds=c(-1,25)))
m2 <- do_admb("tadpole",
data=c(list(nobs=15),tadpoledat),
params=par2,
run.opts=run.control(checkparam="write",
checkdata="write",clean="all"))
par2P <- list(c=list(0.45,bounds=c(0,1),phase=1),
d=list(13,bounds=c(0,50),phase=2),
g=list(1,bounds=c(-1,25),phase=-1))
m2P <- do_admb("tadpole",
data=c(list(nobs=15),tadpoledat),
params=par2P,
run.opts=run.control(checkparam="write",
checkdata="write",clean="all"))
stopifnot(all.equal(m1,m2))
stopifnot(all.equal(m1P,m2P))
unlink("tadpole.tpl")
file.copy(system.file("tplfiles","toy1.tpl",package="R2admb"),"toy1.tpl")
## random effects example??
cbpp <- structure(list(herd = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L,
7L, 7L, 7L, 7L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L,
11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L,
14L, 14L, 15L, 15L, 15L, 15L),
.Label = c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15"),
class = "factor"),
incidence = c(2, 3, 4, 0, 3, 1, 1, 8, 2, 0, 2, 2, 0, 2, 0,
5, 0, 0, 1, 3, 0, 0, 1, 8, 1, 3, 0, 12, 2, 0, 0, 0, 1, 1,
0, 2, 0, 5, 3, 1, 2, 1, 0, 0, 1, 2, 0, 0, 11, 0, 0, 0, 1,
1, 1, 0), size = c(14, 12, 9, 5, 22, 18, 21, 22, 16, 16,
20, 10, 10, 9, 6, 18, 25, 24, 4, 17, 17, 18, 20, 16, 10,
9, 5, 34, 9, 6, 8, 6, 22, 22, 18, 22, 25, 27, 22, 22, 10,
8, 6, 5, 21, 24, 19, 23, 19, 2, 3, 2, 19, 15, 15, 15), period = structure(c(1L,
2L, 3L, 4L, 1L, 2L, 3L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L), .Label = c("1",
"2", "3", "4"), class = "factor")), .Names = c("herd", "incidence",
"size", "period"), row.names = c(NA, 56L), class = "data.frame")
X <- model.matrix(~period,data=cbpp)
Zherd <- model.matrix(~herd-1,data=cbpp)
tmpdat <- list(X=X,Zherd=Zherd,
incidence=cbpp$incidence,size=cbpp$size,
nobs=nrow(cbpp))
d1 <- do_admb("toy1",
data=tmpdat,
params=list(beta=rep(0,ncol(X)),sigma_herd=0.1),
bounds=list(sigma_herd=c(0.0001,20)),
re=list(u_herd=ncol(Zherd)),
run.opts=run.control(checkdata="write",checkparam="write"),
mcmc=TRUE,
mcmc.opts=mcmc.control(mcmc=20,mcmcpars=c("beta","sigma_herd")))
d2 <- do_admb("toy1",
data=tmpdat,
params=list(beta=rep(0,ncol(X)),
sigma_herd=list(0.1,bounds=c(0.0001,20))),
re=list(u_herd=ncol(Zherd)),
run.opts=run.control(checkdata="write",checkparam="write"))
summary(d2)
unlink("toy1.tpl")
}
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