pop & leslie

flr · Oct 14, 2023 · b63ba6b · b63ba6b
1 parent 7261269
commit b63ba6b
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/R/mseMPJabba.R b/R/mseMPJabba.R
@@ -55,7 +55,7 @@ oemFn<-function(om,maxyear=max(dimnames(om)$year),devu=NULL){
   transform(merge(ts,devu,all.x=T),cpue=cpue*exp(residual))[,-6]}
 
 
-jabba2biodyn<-function(object, phase=c("b0"=-1,"r"=4,"k"=3,"p"=-2,"q"=2,"sigma"=1),
+jb2bd<-function(object, phase=c("b0"=-1,"r"=4,"k"=3,"p"=-2,"q"=2,"sigma"=1),
                        min=0.1,max=10){
 
   res=mpb:::biodyn()
@@ -138,7 +138,7 @@ mseMPJabba<-function(om,eq,sa,
                  nt =1,
                  nb =500,
                  nc =2)
-    mp=jabba2biodyn(jb)
+    mp=jb2bd(jb)
     mp=window(mp,end=iYr)
 
     ## Update current year catch

diff --git a/R/popdyn.R b/R/popdyn.R
@@ -22,9 +22,9 @@ utils::globalVariables(c("lhEql","lhPar","lopt","maply","lambda"))
 #' popdyn(par)
 #' }
 
-
+.leslie=leslie   
 popdyn<-function(object,eq=lhEql(lhPar(object))){
-
+  
   par=lhPar(object)
 
   rtn=par[c("linf","k","t0","a50","l50","ato95","a","b","s","v")]
@@ -56,7 +56,7 @@ popdyn<-function(object,eq=lhEql(lhPar(object))){
   rtn=rbind(rtn,lc)
 
   r=maply(seq(dims(eq)$iter), function(x) 
-    log(lambda(leslie(iter(eq,x),fbar=c(refpts(eq)["crash","harvest",x]))[drop=TRUE])))
+    log(lambda(FLife:::leslie(iter(eq,x),fbar=c(refpts(eq)["crash","harvest",x]))[,,1,drop=TRUE])))
   r=FLPar(r=array(c(r),c(1,length(c(r)))))
   rtn=rbind(rtn,r)
 
@@ -120,14 +120,14 @@ popdyn<-function(object,eq=lhEql(lhPar(object))){
   #LF=M
   lfm=FLPar("lfm"=c(0.75*rtn["lc"]+0.25*rtn["linf"]))
   rtn=rbind(rtn,lfm)
-    
+
   r=maply(seq(dims(eq)$iter), function(x) 
-    log(lambda(leslie(iter(eq,x),fbar=c(refpts(eq)["crash","harvest",x]))[drop=TRUE])))
+    log(lambda(FLife:::leslie(iter(eq,x),fbar=c(refpts(eq)["crash","harvest",x]))[,,1,drop=TRUE])))
   r=FLPar(r=array(c(r),c(1,length(c(r)))))
   rtn=rbind(rtn,r)
 
   rc=maply(seq(dims(eq)$iter), function(x) 
-    log(lambda(leslie(iter(eq,x),fbar=c(refpts(eq)["msy","harvest",x]))[drop=TRUE])))
+    log(lambda(FLife:::leslie(iter(eq,x),fbar=c(refpts(eq)["msy","harvest",x]))[,,1,drop=TRUE])))
   rc=FLPar(rc=array(c(rc),c(1,length(c(rc)))))
   rtn=rbind(rtn,rc)