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gadgetLite.R
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library(TMB)
source('estimator.R')
library(parallel)
library(doMC)
library(plyr)
library(dplyr)
registerDoMC(cores=15)
#library(Rgadget)
debug <- FALSE
if(debug){
system('rm *.{o,so}')
compile('gadgetLite.cpp',"-O0 -g",CXX='g++')
dyn.load(dynlib("gadgetLite"))
} else {
compile('gadgetLite.cpp')
dyn.load(dynlib("gadgetLite"))
}
load('runDatrick.RData')
map <- list(recruits=factor(rep(NA,20)),
SIa = factor(rep(NA,4)),
#rickmu = factor(NA),
#ricklambda = factor(NA),
# aComm = factor(NA),
# aSurv = factor(NA),
log_sigma = factor(NA),
initial=factor(rep(NA,9)),
recl=factor(NA),
recsd=factor(NA),
meanrec=factor(NA),
lik_sigma = factor(rep(NA,5)),
linf=factor(NA), bComm=factor(NA), bSurv=factor(NA))
## fixed effects recruits
map.rec <- map
map.rec$recruits <- NULL
## Random effects
mapR <- map
mapR$recruits <- NULL
mapR$log_sigma <- NULL
## sigma estimates
map0 <- llply(gen$parameters,
function(x)
factor(rep(NA,length(x))))
init.par <- gen$parameters
init.par$log_sigma <- log(0.0000001)
design.dat <-
expand.grid(wgts=c(0,1),
exp.type=c('rnd','rick','fixed'),
err=c(0,1),
age=c(0,1)) %>%
filter(!(wgts > 0 & (exp.type!='rnd')),
!(wgts==0 & exp.type=='rnd'))
design.dat$ID <- 1:nrow(design.dat)
run.func <- function(x){
print(x$ID)
if(x$err==1){
dat <- gen.err$data
} else {
dat <- gen$data
}
rnd <- NULL
if(x$exp.type == 'rnd'){
mapGL <- mapR
dat$rfunc <- 1
rnd <- 'recruits'
dat$compW[6] <- x$wgts
} else if(x$exp.type == 'rick'){
mapGL <- map
dat$rfunc <- 1
} else {
mapGL <- map.rec
dat$rfunc <- 0
}
try(mGL(dat,init.par,FALSE,rnd,mapGL),TRUE)
}
#res2 <- dlply(filter(design.dat,exp.type!='rnd'),~ID,run.func,.parallel=TRUE)
#x <- 1
map0$lik_sigma <- NULL
obj0 <- MakeADFun(gen$data,gen$parameters,
map=map,
DLL="gadgetLite")
obj0$hessian <- TRUE
opt0 <- nlminb(obj0$par,obj0$fn,obj0$gr)
pl0 <- obj0$env$parList(opt0$par)
R0 <- obj0$report()
objS <- MakeADFun(gen$data,pl0,
map=map0,
DLL="gadgetLite")
objS$hessian <- TRUE
optS <- nlminb(objS$par,objS$fn,objS$gr)
pl0$lik_sigma <- as.numeric(optS$par)
## remove age data
gen$data$compW[c(3,5)] <- 0
objage <- MakeADFun(gen$data,gen$parameters,
map=map,
DLL="gadgetLite")
objage$hessian <- TRUE
optage <- nlminb(objage$par,objage$fn,objage$gr)
Rage <- objage$report(optage$par)
pl0age <- objage$env$parList(optage$par)
objS <- MakeADFun(gen$data,plage,
map=map0,
DLL="gadgetLite")
objS$hessian <- TRUE
optS <- nlminb(objS$par,objS$fn,objS$gr)
pl0age$lik_sigma <- as.numeric(optS$par)
gen$data$compW[c(3,5)] <- 1
## now with error
gen.err$data$rfunc <- 1
obj.err <- MakeADFun(gen.err$data,gen.err$parameters,
map=map,
DLL="gadgetLite")
obj.err$hessian <- TRUE
opt.err <- nlminb(obj.err$par,obj.err$fn,obj.err$gr)
pl <- obj.err$env$parList(opt.err$par)
objS <- MakeADFun(gen$data,pl,
map=map0,
DLL="gadgetLite")
objS$hessian <- TRUE
optS <- nlminb(objS$par,objS$fn,objS$gr)
pl$lik_sigma <- as.numeric(optS$par)
R.err <- obj.err$report()
## now with error and no age
gen.err$data$compW[c(3,5)] <- 0
obj.errage <- MakeADFun(gen.err$data,gen.err$parameters,
map=map,
DLL="gadgetLite")
obj.errage$hessian <- TRUE
gen.err$data$compW[c(3,5)] <- 1
opt <- nlminb(obj.errage$par,obj.errage$fn,obj.errage$gr)
R.errage <- obj.errage$report()
pl.age <- objage$env$parList(opt$par)
objS <- MakeADFun(gen$data,pl.age,
map=map0,
DLL="gadgetLite")
objS$hessian <- TRUE
optS <- nlminb(objS$par,objS$fn,objS$gr)
pl.age$lik_sigma <- as.numeric(optS$par)
## random effects
gen$data$rfunc <- 1
gen$data$compW <- c(rep(1,5),1)
gen.err$data$rfunc <- 1
gen.err$data$compW <- c(rep(1,5),1)
obj2 <- MakeADFun(gen$data,pl0,random="recruits",
map=mapR,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
tmp <- obj2$par
opt2 <- nlminb(obj2$par,obj2$fn,obj2$gr)
pl2 <- obj2$env$parList(opt2$par)
R2 <- obj2$report()
obj3 <- MakeADFun(gen.err$data,pl,random="recruits",
map=mapR,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
tmp <- obj3$par
upper <- tmp+abs(0.9*tmp)
lower <- tmp-abs(0.9*tmp)
upper['log_sigma'] <- log(0.35)
lower['log_sigma'] <- log(0.05)
opt3 <- nlminb(obj3$par,obj3$fn,obj3$gr)
pl3 <- obj3$env$parList(opt3$par)
R3 <- obj3$report()
gen$data$rfunc <-1
gen$data$compW[c(3,5)] <- 0
obj4 <- MakeADFun(gen$data,pl0age,random="recruits",
map=mapR,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
opt4 <- nlminb(obj4$par,obj4$fn,obj4$gr)
pl4 <- obj4$env$parList(opt4$par)
R4 <- obj4$report()
gen.err$data$rfunc <-1
gen.err$data$compW[6] <- 1
gen.err$data$compW[c(3,5)] <- 0
obj5 <- MakeADFun(gen.err$data,pl.age,random="recruits",
map=mapR,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
opt5 <- nlminb(obj5$par,obj5$fn,obj5$gr)
pl5 <- obj5$env$parList(opt5$par)
R5 <- obj5$report()
## fixed effects
map.rec <- map
map.rec$recruits <- NULL
gen$data$rfunc <- 0
gen.err$data$rfunc <-0
gen.err$data$compW[6] <- 0
gen.err$data$compW[c(3,5)] <- 1
gen$data$compW[6] <- 0
gen$data$compW[c(3,5)] <- 1
obj.rec.err <- MakeADFun(gen.err$data,gen$parameters,
map=map.rec,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
opt.rec.err <- nlminb(obj.rec.err$par,obj.rec.err$fn,obj.rec.err$gr)
pl.rec.err <- obj.rec.err$env$parList(opt.rec.err$par)
R.rec.err <- obj.rec.err$report()
obj.rec <- MakeADFun(gen$data,gen$parameters,
map=map.rec,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
opt.rec <- nlminb(obj.rec$par,obj.rec$fn,obj.rec$gr)
pl.rec <- obj.rec$env$parList(opt.rec$par)
R.rec <- obj.rec$report()
gen.err$data$compW[c(3,5)] <- 0
gen$data$compW[c(3,5)] <- 0
obj.rec.err.age <- MakeADFun(gen.err$data,gen$parameters,
map=map.rec,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
opt.rec.err.age <- nlminb(obj.rec.err.age$par,
obj.rec.err.age$fn,obj.rec.err.age$gr)
pl.rec.err.age <- obj.rec.err.age$env$parList(opt.rec.err.age$par)
R.rec.err.age <- obj.rec.err.age$report()
obj.rec.age <- MakeADFun(gen$data,gen$parameters,
map=map.rec,#list(SIa = factor(rep(NA,4))),
DLL="gadgetLite")
opt.rec.age <- nlminb(obj.rec.age$par,obj.rec.age$fn,obj.rec.age$gr)
pl.rec.age <- obj.rec.age$env$parList(opt.rec.age$par)
R.rec.age <- obj.rec.age$report()
save(opt0,opt.err,optage,opt2,opt3,file='opts.RData')
save(pl0,pl,pl.age,pl0age,pl2,pl3,pl4,pl5,pl.rec,pl.rec.err,
pl.rec.age,pl.rec.err.age,file='pls.RData')
save(R0,Rage,R.err,R.errage,R2,R3,R4,R5,R.rec.err,R.rec.err.age,R.rec,R.rec.age,file='Rs.RData')