#Start from book/chap06 directory
source("datasupport.R")
firstYear<-1851
lastYear<-2010 #changes as needed
sehur<-firstYear:lastYear

readClimate<-function()  #make explicit use function to avoid copying intermediate objects to the global environment R_Global.env (.Global.env)
{
sunspots<-readCov("data/sunspots.txt",header=T,last=T,extrayear=T)
sst<-readCov("data/amon.us.long.mean.txt",header=F,last=T,miss=-99.990,ma="l",extrayear=T)
nao<-readCov("data/nao_jones.txt",last=T,miss=c(-99.99,9999),extrayear=T)  #use nao index?
soi<-readCov("data/soi_ncar.txt",last=T,miss=-99.9,extrayear=T)          #use SOI from ncar. 
return(list(sun=sunspots,sst=sst,nao=nao,soi=soi))                       #can change sun to ssn as needed
}
climateCovariates<-readClimate()

load("best.use.Rdata")
grid<-import.grid("gridboxes.txt") #Regions file
best.use<-add.grid(data=best.use,grid=grid)

Regions=c("Basin","Gulf","Florida","East","US") 
max.regions<-get.max.flags(se=sehur,field="Wmax",rnames=Regions)
save("max.regions",file="max.regions.Rdata") #generates Max.regions

names(max.regions)<-substring(names(max.regions),1,1)
names(max.regions)[names(max.regions)=="U"]<-"US"

months<-list(soi=c(month.abb),
             sst=c(month.abb),
             sun=c(month.abb),
             nao=c(month.abb))
monthsglm<-list(soi=c("Aug","Sep","Oct"),
                sst=c("Aug","Sep","Oct"),
                sun="Sep",nao=c("May","Jun")) #standard months... for simple covariates (nao for Florida May, nao for Gulf, June) dont need additional

covariates<-cbind(make.cov(data=climateCovariates,month=months,separate=T,se=sehur),
                  make.cov(data=climateCovariates,month=monthsglm,separate=F,se=sehur)[-1])
                  
counts<-make.counts.basin(max.regions,se=sehur,single=T)

alldata<-merge(counts,covariates)
save("alldata",file="alldata.Rdata")