library(stockassessment)

oldwd<-setwd("data")

  cn<-read.ices("cn.dat")
  cw<-read.ices("cw.dat")
  dw<-read.ices("dw.dat")
  lw<-read.ices("lw.dat")
  mo<-read.ices("mo.dat")
  nm<-read.ices("nm.dat")
  pf<-read.ices("pf.dat")
  pm<-read.ices("pm.dat")
  sw<-read.ices("sw.dat")
  lf<-read.ices("lf.dat")
  surveys<-read.ices("survey.dat")
  cnA<-read.ices("cn_A.dat")
  cnC<-read.ices("cn_C.dat")
  cnD<-read.ices("cn_D.dat")
  cnF<-read.ices("cn_F.dat")
  cwA<-read.ices("cw_A.dat")
  cwC<-read.ices("cw_C.dat")
  cwD<-read.ices("cw_D.dat")
  cwF<-read.ices("cw_F.dat")

  idx<-!rownames(cn)%in%rownames(cnA)
  sumACDF<-cn[idx,]
  attr(sumACDF, "sumof")<-c(1,2,3,4)
  # temp fix to convergence problems 
  #cnA[cnA==0]<-1; cnA[,1]<-0
  #cnC[cnC==0]<-1
  #cnD[cnD==0]<-1
  #cnF[cnF==0]<-1





  # patch back in time:
  cwA<-rbind(t(t(cw[!rownames(cw)%in%rownames(cwA),])), cwA)
  cwC<-rbind(t(t(cw[!rownames(cw)%in%rownames(cwC),])), cwC)
  cwD<-rbind(t(t(cw[!rownames(cw)%in%rownames(cwD),])), cwD)
  cwF<-rbind(t(t(cw[!rownames(cw)%in%rownames(cwF),])), cwF)


setwd(oldwd)

dat<-setup.sam.data(surveys=surveys,
                    residual.fleet=list(cnA, cnC, cnD, cnF), 
                    sum.residual.fleets=sumACDF,
                    prop.mature=mo, 
                    stock.mean.weight=sw, 
                    catch.mean.weight=list(cwA, cwC, cwD, cwF), 
                    dis.mean.weight=dw, 
                    land.mean.weight=lw,
                    prop.f=pf, 
                    prop.m=pm, 
                    natural.mortality=nm, 
                    land.frac=lf)


save(dat, file="run/data.RData")