Nothing
ypr<-function(age=NULL,wgt=NULL,partial=NULL,M=NULL,plus=FALSE,oldest=NULL,maxF=2,
incrF=0.001,options=c(1),Fsol=NULL,graph=TRUE){
#8/21/2023 add options argument and procedures
if(is.null(age))
stop ("age vectoris missing")
if(is.null(age))
stop ("wgt vector is missing")
if(is.null(partial))
stop ("partial recruitment vector is missing")
if(is.null(M))
stop ("M value or vector is missing")
if(plus==TRUE & is.null(oldest)) stop("oldest must be specified for plus group calculation.")
if(any(length(age)!=c(length(age),length(wgt),length(partial))))
stop("Length of vectors unequal")
if(length(M)==1) M<-rep(M,length(age))
if(length(which(!options %in% c(1,2)))>0) stop("invalid option number")
data<-as.data.frame(cbind(age,wgt,partial,M))
YPR<-as.data.frame(cbind(rep(NA,ceiling(maxF/incrF)+1),rep(NA,ceiling(maxF/incrF)+1)))
names(YPR)<-c("F","YPR")
if(plus==TRUE){
len<-oldest-min(data$age)+1
if(oldest>max(data$age)){
pdata<-data[rep(length(data$age),times=oldest-data$age[length(data$age)]), ]
pdata$age<-seq(max(data$age)+1,oldest,1)
data<-rbind(data,pdata)
}
}
if(plus==FALSE) len<-max(data$age)-min(data$age)+1
if(any(options==1)){
F<-0.0
for(i in 1:length(YPR$F)){
data$S<-exp(-data$partial*F-data$M)
data$psb[1]<-1
for(y in 2:len){
data$psb[y]<-data$S[y-1]
}
data$psb<-cumprod(data$psb)
data$YPR<-((data$partial*F)/(data$partial*F+data$M))*
(1-exp(-data$partial*F-data$M))*data$psb*data$wgt
YPR$YPR[i]<-sum(data$YPR)
YPR$F[i]<-F
F<-F+incrF
}
Ymax<-max(YPR$YPR)
Fmax<-YPR$F[which(YPR$YPR==max(YPR$YPR))]
s10<-((YPR$YPR[2]-YPR$YPR[1])/(YPR$F[2]-YPR$F[1]))*0.10
F10<-Fmax/2;df<-F10/2;ok<-0;fuzz<-0.0001
while (ok==0){
data$s1<-exp(-data$partial*F10-data$M)
data$s1p<-1
for(y in 2:len){
data$s1p[y]<-data$s1[y-1]
}
data$s1p<-cumprod(data$s1p)
d1<-sum(((data$partial*F10)/(data$partial*F10+data$M))*
(1-exp(-data$partial*F10-data$M))*data$s1p*data$wgt)
data$s2<-exp(-data$partial*(F10+0.0001)-data$M)
data$s2p<-1
for(y in 2:len){
data$s2p[y]<-data$s2[y-1]
}
data$s2p<-cumprod(data$s2p)
d2<-sum(((data$partial*(F10+0.0001))/(data$partial*(F10+0.0001)+data$M))*
(1-exp(-data$partial*(F10+0.0001)-data$M))*data$s2p*data$wgt)
slope<-(d2-d1)/((F10+0.0001)-F10)
if(abs(s10-slope)<=fuzz) ok<-1
if(ok==0){
if(slope>s10) F10<-F10+df
if(slope<s10) F10<-F10-df
df<-df/2
}
Y10<-d1
}
}#options==1
#Find YPR for single F
if(any(options==2)){
if(is.null(Fsol)) stop ("Fsol value is missing for option 2.")
data$S<-exp(-data$partial*Fsol-data$M)
data$psb[1]<-1
for(y in 2:len){
data$psb[y]<-data$S[y-1]
}
data$psb<-cumprod(data$psb)
data$YPR<-((data$partial*Fsol)/(data$partial*Fsol+data$M))*
(1-exp(-data$partial*Fsol-data$M))*data$psb*data$wgt
YPR2<-data.frame(F=Fsol,YPR=sum(data$YPR))
}
ans<-NULL
labels<-NULL
if(any(options==1)){
tempo<-data.frame(F=c(F10,Fmax),Yield=c(Y10,Ymax))
rownames(tempo)<-c("F0.10","FMax")
ans<-c(ans,list(tempo))
labels<-c(labels,"Reference_Points")
}
if(any(options==2)){
ans<-c(ans,list(YPR2))
labels<-c(labels,"YPR_at_Fsol")
}
if(any(options==1)){
ans<-c(ans,list(YPR))
labels<-c(labels,"F_vs_YPR")
}
names(ans)<-labels
if(any(options==1) & graph==TRUE) {
plot(YPR[,2]~YPR[,1],ylab="Yield-Per-Recruit",xlab="F",type="l")
}
return(ans)
}
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