scripts/job_submissions/runs_18112017/pernambuco.R

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","pernambuco_confirmed","riograndedonorte_confirmed"),start=c(855,804,862,804,862)-60, end = c(855,804,862,804,862)+60)


maxChain <- 6
versions <- c(1,2, 3)
priors <- NULL
extra_unfixed <- NULL
combos <- expand.grid(runName = "pernambuco_peak", chainNo=1:maxChain,version=versions,stringsAsFactors=FALSE)
jobs_pernambuco <- queuer::enqueue_bulk(obj1, combos, "model_fitting_script",
                                        stateNames="pernambuco",microDat=microDat,
                                        incDat=NULL,preParTab=NULL,
                                        allowablePars=NULL,incStates=NULL,
                                        mcmcPars=mcmcPars,mcmcPars2=mcmcPars2,allPriors=priors,
                                        useInc=FALSE,usePeakTimes=TRUE,covMat=NULL,
                                        peakTimeRange=120,peakTime=804,sim=FALSE, predict=FALSE,
                                        microChain=NULL,prePeakTimes=peakTimes,normLik=FALSE,
                                        stateWeights=NULL,extra_unfixed=extra_unfixed,mosquito_lifespan=5,
                                        do_call=TRUE,timeout=0)

datFile <- "~/Documents/Zika/Data/brazil/microceph_reports_2016_confirmed.csv"
microDat <- read.csv(datFile,stringsAsFactors=FALSE)
combos <- expand.grid(runName = "pernambuco_peak_confirmed2", chainNo=1:maxChain,version=versions,stringsAsFactors=FALSE)
jobs_pernambuco <- queuer::enqueue_bulk(obj1, combos, "model_fitting_script",
                                        stateNames="pernambuco",microDat=microDat,
                                        incDat=NULL,preParTab=NULL,
                                        allowablePars=NULL,incStates=NULL,
                                        mcmcPars=mcmcPars,mcmcPars2=mcmcPars2,allPriors=priors,
                                        useInc=FALSE,usePeakTimes=TRUE,covMat=NULL,
                                        peakTimeRange=120,peakTime=804,sim=FALSE, predict=FALSE,
                                        microChain=NULL,prePeakTimes=peakTimes,normLik=FALSE,
                                        stateWeights=NULL,extra_unfixed=extra_unfixed,mosquito_lifespan=5,
                                        do_call=TRUE,timeout=0)
jameshay218/zikaProj documentation built on Jan. 9, 2020, 7:26 p.m.