Nothing
R/CatDynPar.R
In CatDyn: Fishery Stock Assessment by Catch Dynamics Models
CatDynPar <-
function(x,method,partial=TRUE)
{
if(class(x) != "catdyn")
{stop("'x' must be an object of class 'catdyn' (created by function CatDynFit)")}
sdistr.set <- c("poisson","apnormal","aplnormal")
if(x$Data$Properties$Units["Time Step"]=="month")
{
#Month 1 Fleet
if(length(x$Data$Properties$Fleets$Fleet)==1)
{
month.F1 <- x$Model[[method]]$Dates[2:(x$Model[[method]]$Type+1)]
years.F1 <- as.numeric(format(as.Date(x$Data$Properties$Dates["StartDate"]),"%Y"))+floor(month.F1/12)
month.F1 <- as.integer((month.F1/12-floor(month.F1/12))*12)
#Month 1 Fleet Likelihood without dispersion
if(x$Model[[method]]$Distr%in%sdistr.set)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",paste(years.F1,month.F1,sep="-"),"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
#Month 1 Fleet Likelihood with dispersion
if(!x$Model[[method]]$Distr%in%sdistr.set)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
#end of Month 1 Fleet
}
#Month 2 Fleets
if(length(x$Data$Properties$Fleets$Fleet)==2)
{
month.F1 <- x$Model[[method]]$Dates[2:(x$Model[[method]]$Type[1]+1)]
month.F2 <- x$Model[[method]]$Dates[(x$Model[[method]]$Type[1]+2):(x$Model[[method]]$Type[1]+1+x$Model[[method]]$Type[2])]
years.F1 <- as.numeric(format(as.Date(x$Data$Properties$Dates["StartDate"]),"%Y"))+floor(month.F1/12)
years.F2 <- as.numeric(format(as.Date(x$Data$Properties$Dates["StartDate"]),"%Y"))+floor(month.F2/12)
month.F1 <- as.integer((month.F1/12-floor(month.F1/12))*12)
month.F2 <- as.integer((month.F2/12-floor(month.F2/12))*12)
if(any(month.F1==0)){month.F1[which(month.F1==0)] <- 12}
if(any(month.F2==0)){month.F2[which(month.F2==0)] <- 12}
#Month 2 Fleets Both fleets with likelihood without dispersion (sdristr.set)
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==2)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","",""),
Estimates.F1=unlist(x$Model[[method]]$bt.par[1:(2+length(years.F1)+3)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[1:(2+length(years.F1)+3)])/
unlist(x$Model[[method]]$bt.par[1:(2+length(years.F1)+3)]),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.par))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+4):(length(x$Model[[method]]$bt.stdev)))])/
unlist(x$Model[[method]]$bt.par[(c(1,2,(2+length(years.F2)+4):length(x$Model[[method]]$bt.par)))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#Month 2 Fleets First fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==-1)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3))]),NA),
CVpCent.F1=round(c(100*unlist(x$Model[[method]]$bt.stdev[c(1:(2+length(years.F1)+3))])/
unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3))]),NA),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.par))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.stdev))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.par))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#Month 2 Fleets Second fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==1)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par)))]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.stdev)))])/
unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par)))]),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-1))]),NA),
CVpCent.F2=c(round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.stdev)-1))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-1))]),1),NA),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#Month 2 Fleets Both fleets with likelihood with dispersion
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==0)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par))-1)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.stdev))-1)])/
unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par))-1)]),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-2),(length(x$Model[[method]]$bt.par)))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.stdev)-2),(length(x$Model[[method]]$bt.stdev)))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-2),(length(x$Model[[method]]$bt.par)))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#End of Month 2 Fleets
}
#End of month
}
if(x$Data$Properties$Units["Time Step"]=="day" | x$Data$Properties$Units["Time Step"]=="week")
{
#Week/Day 1 Fleet
if(length(x$Data$Properties$Fleets$Fleet)==1)
{
#Week/Day 1 fleet Pure depletion
if(x$Model[[method]]$Type==0)
{
#Week/Day 1 fleet Pure depletion Likelihood without dispersion
if(x$Model[[method]]$Distr%in%sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
#Week/Day 1 fleet Pure depletion Likelihood with dispersion
if(!x$Model[[method]]$Distr%in%sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
#End of Week/Day 1 fleet Pure depletion
}
if(x$Model[[method]]$Type!=0)
#Week/Day 1 fleet With perturbations
{
#Week/Day 1 fleet With perturbations Likelihood without dispersion
waves <- abs(x$Model[[method]]$Type)
if(x$Model[[method]]$Distr %in% sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
finalweek.year1 <- as.numeric(format(as.Date(paste(year1,"-12-31",sep="")), "%W"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
#weeks <- x$Model[[method]]$Dates[2:(waves+1)]
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
#dates.ranges <- vector("character",waves)
if(partial & x$Model[[method]]$Type < 0)
{
dates.ranges <- vector("character",2*waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)] - finalweek.year1
for(w in 1:2*waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)]
for(w in 1:(2*waves))
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",dates.ranges,"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
dates.ranges <- vector("character",waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)] - finalweek.year1
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
for(w in 1:(waves))
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",dates.ranges,"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
dates.ranges <- vector("character",waves)
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",dates.ranges,"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
if(partial & x$Model[[method]]$Type < 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+2)]),
"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),
"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
}
#Week/Day 1 fleet With perturbations Likelihood with dispersion
if(!x$Model[[method]]$Distr %in% sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
finalweek.year1 <- as.numeric(format(as.Date(paste(year1,"-12-31",sep="")), "%W"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(partial & x$Model[[method]]$Type < 0)
{
dates.ranges <- vector("character",2*waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)] - finalweek.year1
for(w in 1:2*waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)]
for(w in 1:2*waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",dates.ranges,"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
dates.ranges <- vector("character",waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)] - finalweek.year1
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",dates.ranges,"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
dates.ranges <- vector("character",waves)
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",dates.ranges,"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
if(partial & x$Model[[method]]$Type < 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+2)]),
"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),
"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
}
#End of Week/Day 1 fleet With perturbations
}
#End of Week/Day one fleet
}
#Week/Day 2 Fleets
if(length(x$Data$Properties$Fleets$Fleet)==2)
{
#Week/Day 2 Fleets Pure depletion
if(sum(x$Model[[method]]$Type)==0)
{
#Week/Day 2 Fleets Pure depletion Both fleets with likelihood without dispersion
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==2)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=unlist(x$Model[[method]]$bt.par[1:5]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[1:5])/
unlist(x$Model[[method]]$bt.par[1:5]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=unlist(x$Model[[method]]$bt.par[1:5]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[1:5])/
unlist(x$Model[[method]]$bt.par[1:5]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Week/Day 2 Fleets Pure depletion First fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==-1)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[1:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[1:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[1:5]),NA),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:9)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[1:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[1:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[1:5]),NA),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:9)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Week/Day 2 Fleets Pure depletion Second fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==1)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Week/Day 2 Fleets Pure depletion Both fleets with likelihood with dispersion
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==0)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8,10)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8,10)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#End of Week/Day 2 Fleets Pure depletion
}
if(sum(x$Model[[method]]$Type)!=0)
#Week/Day 2 Fleets With perturbations
{
year <- as.numeric(substring(x$Data$Properties$Dates[["StartDate"]],1,4))
waves.F1 <- x$Model[[method]]$Type[1]
waves.F2 <- x$Model[[method]]$Type[2]
#Week/Day 2 Fleets With perturbations Both fleets with likelihood without dispersion (sdristr.set)
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==2)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),1),
Timing.F2=c("","",dates.ranges.F2,"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Timing.F1=c("","",dates.ranges.F1,rep("",3+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),1),
Timing.F2=c("","",dates.ranges.F2,"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",3+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(waves.F1+6):(waves.F1+5+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(waves.F1+6):(waves.F1+5+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
#First fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==-1)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",dates.ranges.F1,rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+4))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+4))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+4))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(waves.F1+6):((waves.F1+6+waves.F2+3)))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(waves.F1+6):((waves.F1+6+waves.F2+3)))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(waves.F1+6):((waves.F1+6+waves.F2+3)))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
#Second fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==1)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+length(waves.F2)+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",dates.ranges.F1,rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
#Both fleets with likelihood with dispersion
else if(sum(x$Model[[method]]$Distr%in%sdistr.set)==0)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
else if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",dates.ranges.F1,rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
}
#End of two fleets
}
#End of week/day time step
}
return(partable)
#End of function
}
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CatDynPar <-
function(x,method,partial=TRUE)
{
if(class(x) != "catdyn")
{stop("'x' must be an object of class 'catdyn' (created by function CatDynFit)")}
sdistr.set <- c("poisson","apnormal","aplnormal")
if(x$Data$Properties$Units["Time Step"]=="month")
{
#Month 1 Fleet
if(length(x$Data$Properties$Fleets$Fleet)==1)
{
month.F1 <- x$Model[[method]]$Dates[2:(x$Model[[method]]$Type+1)]
years.F1 <- as.numeric(format(as.Date(x$Data$Properties$Dates["StartDate"]),"%Y"))+floor(month.F1/12)
month.F1 <- as.integer((month.F1/12-floor(month.F1/12))*12)
#Month 1 Fleet Likelihood without dispersion
if(x$Model[[method]]$Distr%in%sdistr.set)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",paste(years.F1,month.F1,sep="-"),"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
#Month 1 Fleet Likelihood with dispersion
if(!x$Model[[method]]$Distr%in%sdistr.set)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
#end of Month 1 Fleet
}
#Month 2 Fleets
if(length(x$Data$Properties$Fleets$Fleet)==2)
{
month.F1 <- x$Model[[method]]$Dates[2:(x$Model[[method]]$Type[1]+1)]
month.F2 <- x$Model[[method]]$Dates[(x$Model[[method]]$Type[1]+2):(x$Model[[method]]$Type[1]+1+x$Model[[method]]$Type[2])]
years.F1 <- as.numeric(format(as.Date(x$Data$Properties$Dates["StartDate"]),"%Y"))+floor(month.F1/12)
years.F2 <- as.numeric(format(as.Date(x$Data$Properties$Dates["StartDate"]),"%Y"))+floor(month.F2/12)
month.F1 <- as.integer((month.F1/12-floor(month.F1/12))*12)
month.F2 <- as.integer((month.F2/12-floor(month.F2/12))*12)
if(any(month.F1==0)){month.F1[which(month.F1==0)] <- 12}
if(any(month.F2==0)){month.F2[which(month.F2==0)] <- 12}
#Month 2 Fleets Both fleets with likelihood without dispersion (sdristr.set)
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==2)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","",""),
Estimates.F1=unlist(x$Model[[method]]$bt.par[1:(2+length(years.F1)+3)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[1:(2+length(years.F1)+3)])/
unlist(x$Model[[method]]$bt.par[1:(2+length(years.F1)+3)]),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.par))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+4):(length(x$Model[[method]]$bt.stdev)))])/
unlist(x$Model[[method]]$bt.par[(c(1,2,(2+length(years.F2)+4):length(x$Model[[method]]$bt.par)))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#Month 2 Fleets First fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==-1)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3))]),NA),
CVpCent.F1=round(c(100*unlist(x$Model[[method]]$bt.stdev[c(1:(2+length(years.F1)+3))])/
unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3))]),NA),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.par))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.stdev))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):length(x$Model[[method]]$bt.par))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#Month 2 Fleets Second fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==1)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par)))]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.stdev)))])/
unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par)))]),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-1))]),NA),
CVpCent.F2=c(round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.stdev)-1))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-1))]),1),NA),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#Month 2 Fleets Both fleets with likelihood with dispersion
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==0)
{
partable <- data.frame(Parameter=c("M.1/month",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".",years.F1,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",paste(years.F1,month.F1,sep="-"),"","","",""),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par))-1)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.stdev))-1)])/
unlist(x$Model[[method]]$bt.par[c(1:(2+length(years.F1)+3),length(unlist(x$Model[[method]]$bt.par))-1)]),1),
Timing.F2=c("","",paste(years.F2,month.F2,sep="-"),"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-2),(length(x$Model[[method]]$bt.par)))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.stdev)-2),(length(x$Model[[method]]$bt.stdev)))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+length(years.F2)+3+1):(length(x$Model[[method]]$bt.par)-2),(length(x$Model[[method]]$bt.par)))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
#End of Month 2 Fleets
}
#End of month
}
if(x$Data$Properties$Units["Time Step"]=="day" | x$Data$Properties$Units["Time Step"]=="week")
{
#Week/Day 1 Fleet
if(length(x$Data$Properties$Fleets$Fleet)==1)
{
#Week/Day 1 fleet Pure depletion
if(x$Model[[method]]$Type==0)
{
#Week/Day 1 fleet Pure depletion Likelihood without dispersion
if(x$Model[[method]]$Distr%in%sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
#Week/Day 1 fleet Pure depletion Likelihood with dispersion
if(!x$Model[[method]]$Distr%in%sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
#End of Week/Day 1 fleet Pure depletion
}
if(x$Model[[method]]$Type!=0)
#Week/Day 1 fleet With perturbations
{
#Week/Day 1 fleet With perturbations Likelihood without dispersion
waves <- abs(x$Model[[method]]$Type)
if(x$Model[[method]]$Distr %in% sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
finalweek.year1 <- as.numeric(format(as.Date(paste(year1,"-12-31",sep="")), "%W"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
#weeks <- x$Model[[method]]$Dates[2:(waves+1)]
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
#dates.ranges <- vector("character",waves)
if(partial & x$Model[[method]]$Type < 0)
{
dates.ranges <- vector("character",2*waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)] - finalweek.year1
for(w in 1:2*waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)]
for(w in 1:(2*waves))
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",dates.ranges,"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
dates.ranges <- vector("character",waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)] - finalweek.year1
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
for(w in 1:(waves))
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",dates.ranges,"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
dates.ranges <- vector("character",waves)
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",dates.ranges,"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
if(partial & x$Model[[method]]$Type < 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+2)]),
"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),
"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta"),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),"","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
}
#Week/Day 1 fleet With perturbations Likelihood with dispersion
if(!x$Model[[method]]$Distr %in% sdistr.set)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
finalweek.year1 <- as.numeric(format(as.Date(paste(year1,"-12-31",sep="")), "%W"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(partial & x$Model[[method]]$Type < 0)
{
dates.ranges <- vector("character",2*waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)] - finalweek.year1
for(w in 1:2*waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(2*waves+1)]
for(w in 1:2*waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",dates.ranges,"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
dates.ranges <- vector("character",waves)
if(year2 > year1)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)] - finalweek.year1
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year2, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
if(year2 == year1)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Recruitment.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",dates.ranges,"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
weeks <- x$Model[[method]]$Dates[2:(waves+1)]
dates.ranges <- vector("character",waves)
for(w in 1:waves)
{
dates.ranges[w] <- paste(range(days[sprintf("%d %02d", year1, weeks[w]) == format(days, "%Y %U")]),collapse=' ')
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",dates.ranges,"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
if(partial & x$Model[[method]]$Type < 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("Spawning.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+2)]),
"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(partial & x$Model[[method]]$Type > 0)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),
"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
if(!partial)
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units,sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves+1)]),"","","",""),
Estimates=unlist(x$Model[[method]]$bt.par),
CVpCent=round(100*unlist(x$Model[[method]]$bt.stdev)/unlist(x$Model[[method]]$bt.par),1),row.names=NULL)
}
}
}
#End of Week/Day 1 fleet With perturbations
}
#End of Week/Day one fleet
}
#Week/Day 2 Fleets
if(length(x$Data$Properties$Fleets$Fleet)==2)
{
#Week/Day 2 Fleets Pure depletion
if(sum(x$Model[[method]]$Type)==0)
{
#Week/Day 2 Fleets Pure depletion Both fleets with likelihood without dispersion
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==2)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=unlist(x$Model[[method]]$bt.par[1:5]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[1:5])/
unlist(x$Model[[method]]$bt.par[1:5]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=unlist(x$Model[[method]]$bt.par[1:5]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[1:5])/
unlist(x$Model[[method]]$bt.par[1:5]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Week/Day 2 Fleets Pure depletion First fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==-1)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[1:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[1:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[1:5]),NA),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:9)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[1:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[1:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[1:5]),NA),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:9)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:9)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Week/Day 2 Fleets Pure depletion Second fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==1)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:8)]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Week/Day 2 Fleets Pure depletion Both fleets with likelihood with dispersion
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==0)
{
if(x$Data$Properties$Units["Time Step"]=="week")
{
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8,10)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=unlist(x$Model[[method]]$bt.par[c(1:5,9)]),
CVpCent.F1=round(100*unlist(x$Model[[method]]$bt.stdev[c(1:5,9)])/
unlist(x$Model[[method]]$bt.par[c(1:5,9)]),1),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:8,10)])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:8,10)]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:5] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#End of Week/Day 2 Fleets Pure depletion
}
if(sum(x$Model[[method]]$Type)!=0)
#Week/Day 2 Fleets With perturbations
{
year <- as.numeric(substring(x$Data$Properties$Dates[["StartDate"]],1,4))
waves.F1 <- x$Model[[method]]$Type[1]
waves.F2 <- x$Model[[method]]$Type[2]
#Week/Day 2 Fleets With perturbations Both fleets with likelihood without dispersion (sdristr.set)
if(sum(x$Model[[method]]$Distr%in%sdistr.set)==2)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),1),
Timing.F2=c("","",dates.ranges.F2,"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5])),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Timing.F1=c("","",dates.ranges.F1,rep("",3+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),1),
Timing.F2=c("","",dates.ranges.F2,"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta"),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",3+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)])),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(waves.F1+6):(waves.F1+5+waves.F2+3))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(waves.F1+6):(waves.F1+5+waves.F2+3))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
#First fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==-1)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),NA),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",dates.ranges.F1,rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+4))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+4))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+4):(2+waves.F1+3+waves.F2+4))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),NA),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","","",""),
Estimates.F2=unlist(x$Model[[method]]$bt.par[c(1,2,(waves.F1+6):((waves.F1+6+waves.F2+3)))]),
CVpCent.F2=round(100*unlist(x$Model[[method]]$bt.stdev[c(1,2,(waves.F1+6):((waves.F1+6+waves.F2+3)))])/
unlist(x$Model[[method]]$bt.par[c(1,2,(waves.F1+6):((waves.F1+6+waves.F2+3)))]),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
#Second fleet with likelihood without dispersion
if(diff(x$Model[[method]]$Distr%in%sdistr.set)==1)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+length(waves.F2)+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",dates.ranges.F1,rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),1)),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA)/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),NA),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
#Both fleets with likelihood with dispersion
else if(sum(x$Model[[method]]$Distr%in%sdistr.set)==0)
{
#Only second fleet with perturbations
if(waves.F1==0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2)]),rep(0,waves.F2),unlist(x$Model[[method]]$bt.stdev[3:5]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2)]),rep(1,waves.F2),unlist(x$Model[[method]]$bt.par[3:5]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F2+1)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,6:(5+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:3] <- paste(c("Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[4:6] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
#Both fleets with perturbations
else if(waves.F1!=0 & waves.F2!=0)
{
year1 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["StartDate"]]), "%Y"))
year2 <- as.numeric(format(as.Date(x$Data$Properties$Dates[["EndDate"]]), "%Y"))
days <- as.Date(paste(year1, 1, 1, sep = "-"))+0:365*(year2-year1+1)
if(x$Data$Properties$Units["Time Step"]=="week")
{
weeks1 <- x$Model[[method]]$Dates[2:(waves.F1+1)]
weeks2 <- x$Model[[method]]$Dates[2:(waves.F2+1)]
dates.ranges.F1 <- vector("character",waves.F1)
dates.ranges.F2 <- vector("character",waves.F2)
for(w in 1:waves.F1)
{
if(weeks1[w] <= 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year1, weeks1[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks1[w] > 53)
{
dates.ranges.F1[w] <- paste(range(days[sprintf("%d %02d", year2, weeks1[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
for(w in 1:waves.F2)
{
if(weeks2[w] <= 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year1, weeks2[w]) == format(days, "%Y %U")]),collapse=' ')
}
if(weeks2[w] > 53)
{
dates.ranges.F2[w] <- paste(range(days[sprintf("%d %02d", year2, weeks2[w]-53) == format(days, "%Y %U")]),collapse=' ')
}
}
partable <- data.frame(Parameter=c("M.1/week",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",dates.ranges.F1,rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",dates.ranges.F2,"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
if(x$Data$Properties$Units["Time Step"]=="day")
{
partable <- data.frame(Parameter=c("M.1/day",
paste("N0.",x$Data$Properties$Units["NumbersMultiplier"],sep=""),
paste("Rec.",x$Data$Properties$Units["NumbersMultiplier"],".Wave",1:waves.F2,sep=""),
paste("k.1/",x$Data$Properties$Fleets$Units[1],sep=""),
"alpha","beta",
paste("psi.",x$Data$Properties$Units["NumbersMultiplier"],".squared",sep="")),
Timing.F1=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[2:(waves.F1+1)]),rep("",4+waves.F2-waves.F1)),
Estimates.F1=c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),
CVpCent.F1=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.stdev[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.stdev),2)[1])/
c(unlist(x$Model[[method]]$bt.par[c(1,2,3:(waves.F1+2))]),rep(0,waves.F2-waves.F1),unlist(x$Model[[method]]$bt.par[(waves.F1+3):(waves.F1+5)]),tail(unlist(x$Model[[method]]$bt.par),2)[1]),1),
Timing.F2=c("","",as.character(as.Date(x$Data$Properties$Dates[["StartDate"]])+x$Model[[method]]$Dates[(waves.F1+2):(waves.F1+1+waves.F2)]),"","","",""),
Estimates.F2=c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),
CVpCent.F2=round(100*c(unlist(x$Model[[method]]$bt.stdev[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.stdev),1))/
c(unlist(x$Model[[method]]$bt.par[c(1,2,(2+waves.F1+3+1):(2+waves.F1+3+waves.F2+3))]),tail(unlist(x$Model[[method]]$bt.par),1)),1),row.names=NULL)
names(partable)[2:4] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[1],sep="")
names(partable)[5:7] <- paste(c("Timing.","Estimates.","CVpCent."),x$Data$Properties$Fleets$Fleet[2],sep="")
}
}
}
}
#End of two fleets
}
#End of week/day time step
}
return(partable)
#End of function
}
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