scripts/job_submissions/runs_18112017/bahia.R

In jameshay218/zikaProj: zikaInfer

datFile <- "~/Documents/Zika/Data/brazil/microceph_reports_2016.csv"
incFile <- "~/Documents/Zika/Data/brazil/brazil_report_zikv_inc_2016.csv"
microDat <- read.csv(datFile,stringsAsFactors=FALSE)
incDat <- read.csv(incFile,stringsAsFactors=FALSE)
peakTimes <- data.frame(local=c("bahia","pernambuco","riograndedonorte"),start=c(855,804,862)-60, end = c(855,804,862)+60)
maxChain <- 5
versions <- c(1,2)
priors <- NULL
extra_unfixed <- NULL

combos <- expand.grid(runName = "bahia", chainNo=1:maxChain,version=versions,stringsAsFactors=FALSE)
jobs_bahia <- queuer::enqueue_bulk(obj1, combos, "model_fitting_script",
                                  stateNames="bahia",microDat=microDat,incDat=incDat,preParTab=NULL,
                                  allowablePars=NULL,incStates=NULL,
                                  mcmcPars=mcmcPars,mcmcPars2=mcmcPars2,allPriors=priors,
                                  useInc=TRUE,usePeakTimes=FALSE,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)

combos <- expand.grid(runName = "bahia_peak", chainNo=1:maxChain,version=versions,stringsAsFactors=FALSE)
jobs_bahia <- queuer::enqueue_bulk(obj1, combos, "model_fitting_script",
                                  stateNames="bahia",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)