three_states <- c("bahia","pernambuco","riograndedonorte")
microDatFile <- "~/Documents/Zika/Data/brazil/brazil_microCeph_28022017.csv"
microDat <- read.csv(microDatFile,stringsAsFactors=FALSE)
microDat <- microDat[microDat$startDay < 1214,]
incDat <- NULL
## Generate peak times
peakTimes <- data.frame(local=three_states,start=c(855,804,862)-30, end = c(855,804,862)+30)
####################
## Report data runs
####################
maxChain <- 5
versions <- c(1,2,3)
priors <- NULL
extra_unfixed <- NULL
combos <- expand.grid(runName = "multi_3", chainNo=1:maxChain,version=versions,stringsAsFactors=FALSE)
jobsA <- queuer::enqueue_bulk(obj1, combos, "model_fitting_script",
stateNames=three_states,microDat=microDat,incDat=incDat,preParTab=NULL,
allowablePars=NULL,incStates=NULL,
mcmcPars=mcmcPars,mcmcPars2=mcmcPars2,allPriors=priors,
useInc=FALSE,usePeakTimes=TRUE,covMat=NULL,
peakTimeRange=NULL,peakTime=NULL,sim=FALSE, predict=FALSE,
microChain=NULL,prePeakTimes=peakTimes,normLik=FALSE,
stateWeights=NULL,extra_unfixed=extra_unfixed,mosquito_lifespan=5,
do_call=TRUE,timeout=0)
priors <- function(values){
names(values) <- names
d_eh <- dnorm(values["D_EH"],5,0.94,1)
d_em <- dnorm(values["D_EM"], 8.2, 1.12,1)
d_ih <- dnorm(values["D_IH"], 4.7, 0.51,1)
return(sum(d_eh, d_em, d_ih))
}
extra_unfixed <- c("D_EH","D_EM","D_IH")
combos <- expand.grid(runName = "multi_3_varied", chainNo=1:maxChain,version=versions,stringsAsFactors=FALSE)
jobsB <- queuer::enqueue_bulk(obj1, combos, "model_fitting_script",
stateNames=three_states,microDat=microDat,incDat=incDat,preParTab=NULL,
allowablePars=NULL,incStates=NULL,
mcmcPars=mcmcPars,mcmcPars2=mcmcPars2,allPriors=priors,
useInc=FALSE,usePeakTimes=TRUE,covMat=NULL,
peakTimeRange=NULL,peakTime=NULL,sim=FALSE, predict=FALSE,
microChain=NULL,prePeakTimes=peakTimes,normLik=FALSE,
stateWeights=NULL,extra_unfixed=extra_unfixed,do_call=TRUE,timeout=0)
jobs_multi3 <- list(jobsA,jobsB)
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