#x="/home/laurie/Desktop/Dropbox/ICCAT/SCRS/BIL/2012/section_6/Inputs/SS3/mcmc_diagnostics/Run_1"
utils::globalVariables(c("SS_output","FleetName","Yr","Obs","Exp","Dev","index","residual",".diagUbsp"))
utils::globalVariables(c("ddply"))
utils::globalVariables(c("."))
utils::globalVariables(c("diagsFn"))
.diagUss=function(x,ncols=320){
res=subset(SS_output(x, forecast =FALSE,
covar =FALSE,
checkcor =FALSE,
verbose =FALSE,
printstats=FALSE,
hidewarn =TRUE,
NoCompOK =TRUE,ncols=ncols)$cpue, !is.na(Dev),select=c(Fleet_name,Yr,Seas,Obs,Exp,Dev,SE))
names(res)=c("name","year","season","obs","hat","residual","se")
res=subset(ddply(res,.(name,season),diagsFn),!is.na(residual))
res}
#
# if (FALSE){
# ### SS3
# rns=c("/home/lkell/Dropbox/MyStuff/WHM/analysis/Inputs/SS3_Final2/Run_1",
# "/home/lkell/Dropbox/MyStuff/WHM/analysis/Inputs/SS3_Final2/Run_2",
# "/home/lkell/Dropbox/MyStuff/WHM/analysis/Inputs/SS3_Final2/Run_3",
# "/home/lkell/Dropbox/MyStuff/WHM/analysis/Inputs/SS3_Final2/Run_4",
# "/home/lkell/Dropbox/MyStuff/WHM/analysis/Inputs/SS3_Final2/Run_5")
#
# tm=SS_output(rns[1])
#
# ssCpue=fnDiags(transform(tm$cpue, year=Yr, cpue=Fleet, obs=Obs, hat=Exp, residual=log(Obs/Exp))[,c("year","cpue","obs","hat","residual")])
# ssCpue=merge(ssCpue,transform(tm$timeseries, year=Yr, stock=Bio_all)[,c("year","stock")])
# ssCpue=merge(ssCpue,ssU)
#
# rm(SS_output)
# rm(SS_plots)
# update_r4ss_files()
#
# #no hessian
# rm(myreplist)
# myreplist <- SS_output(dir = "C:\\Work\\Assess\\ICCAT\\BUM\\SS\\7_2sex_v320",
# printstats = T, covar=F, cormax=0.70, forecast=F,printhighcor=50, printlowcor=50)
# SS_plots(replist = myreplist,plot=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,18,22:49),
# uncertainty=F, sprtarg=0.40, btarg=0.4, datplot=F, minbthresh=-1)
# print = 1:49, printfolder="R_plots", dir="default", pdf=F,
#
#
# #with hessian
# rm(myreplist)
# myreplist <- SS_output(dir = "C:\\Work\\Assess\\ICCAT\\BUM\\SS\\7_2sex_v320",
# printstats = T, covar=T, cormax=0.70, forecast=F,printhighcor=50, printlowcor=50)
# SS_plots(replist = myreplist,plot=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,18,22:49),
# uncertainty=T, sprtarg=0.40, btarg=0.4, datplot=F, minbthresh=-1
# ,print = 1:49, printfolder="R_plots", dir="default")
#
# SSplotPars(dir = "C:\\Work\\Assess\\ICCAT\\BUM\\SS\\Copy of 6_2sex_v320", fitrange=F)
# }
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