Merge branch 'master' of github.com:flr/FLife

R/omOut.R

@@ -1,16 +1,22 @@
 omStock<-function(object){
-  ageSwt<-function(object) apply(stock.n(object)%*%ages(stock.n(object)),2:6,sum)%/%
+  sage<-function(object) apply(stock.n(object)%*%ages(stock.n(object)),2:6,sum)%/%
                            apply(stock.n(object),2:6,sum)
-  ageCwt<-function(object) apply(catch.n(object)%*%ages(catch.n(object)),2:6,sum)%/%
+  cage<-function(object) apply(catch.n(object)%*%ages(catch.n(object)),2:6,sum)%/%
                            apply(catch.n(object),2:6,sum) 
+  swt<-function(object) apply(stock.n(object)%*%stock.wt(object),2:6,sum)%/%
+    apply(stock.n(object),2:6,sum)
+  cwt<-function(object) apply(catch.n(object)%*%catch.wt(object),2:6,sum)%/%
+    apply(catch.n(object),2:6,sum) 
   hvt   <-function(object) catch(object)/stock(object)
 
   recs  <-function(object) {res=rec(object)
                             dimnames(res)[[1]]="all"
                             res}
+
+  catchJuv<-function(object) apply(catch.n(object)%*%(1-mat(object))%*%catch.wt(object),2:6,sum)
 
   res=FLQuants(object,"ssb"=ssb,"stock"=stock,"rec"=recs,"catch"=catch,"fbar"=fbar,
-                      "ageSwt"=ageSwt,"ageCwt"=ageCwt,"hrate"=hvt)
+                      "swt"=swt,"cwt"=cwt,"sage"=sage,"cage"=cage,"catchJuv"=catchJuv)
 
   model.frame(mcf(res),drop=TRUE)}
 
@@ -23,13 +29,25 @@ omRefs<-function(object){
 
   refs}
 
-omSmry<-function(x,y="missing"){
+
+omSmry<-function(x,y="missing",z="missing"){
 
   res=omStock(x)
 
   if ("FLBRP" %in% is(y))
     res=merge(res,omRefs(refpts(y)))
-  else if ("FLPar" %in% is(y))
+  else if ("FLPar" %in% is(y))  
     res=merge(res,omRefs(y))
 
+  if ("FLPar" %in% is(z))
+    if (all(c("a","b") %in% dimnames(z)$params))
+      res=merge(res,lenFn(x,z))
   return(res)}
+
+lenFn<-function(x,y){
+  sln<-function(object) apply(stock.n(object)%*%exp(log(stock.wt(object)%/%y["a"])%/%y["b"]),2:6,sum)%/%
+    apply(stock.n(object),2:6,sum)
+  cln<-function(object) apply(catch.n(object)%*%exp(log(catch.wt(object)%/%y["a"])%/%y["b"]),2:6,sum)%/%
+    apply(catch.n(object),2:6,sum) 
+
+  model.frame(FLQuants(x,"sln"=sln,"cln"=cln),drop=TRUE)}

R/swon.R

@@ -0,0 +1,8 @@
+Six operational objectives are: 
+
+1. stock has a greater than ___% probability of occurring in the green quadrant of the Kobe matrix for (period). 
+2. stock has a less than ___% probability of entering the red quadrant of the Kobe matrix for (period). 
+3. less than ___% probability of the NSWO stock falling below BLIM (to be defined) for (period). 
+4. Maximize catch levels,  achieving BMSY. 
+5. Limit change in TAC to ___% between management periods. 
+6. Ensure that fishing mortality of juveniles is below ___ for (period).