after check

DESCRIPTION

@@ -14,14 +14,13 @@ Description: Many studies have shown the relationships between life history
 LazyData: true
 License: GPL (>= 2)
 Depends:
-  	R(>= 3.1),
+    R(>= 3.1),
     FLCore (>= 2.6),
 Imports:
     FLBRP,
     methods,
     popbio,
-    plyr,
-    reshape
+    plyr
 Suggests:
     ggplotFL (>= 2.5),
     testthat,
@@ -79,4 +78,6 @@ Collate:
     getScriptPath.R
     pMeasure.R
     sim.R
+    knifeEdgeMsy.R
+    netSel.r
 RoxygenNote: 6.0.1

NAMESPACE

@@ -14,6 +14,7 @@ exportMethods(gascuel)
 exportMethods(gislason)
 exportMethods(gompertz)
 exportMethods(griffiths)
+exportMethods(grwdd)
 exportMethods(jensen)
 exportMethods(jensen2)
 exportMethods(knife)
@@ -34,17 +35,16 @@ exportMethods(richards)
 exportMethods(rikhter)
 exportMethods(rikhter2)
 exportMethods(rnoise)
-exportMethods(rlnoise)
 exportMethods(rod)
 exportMethods(roff)
 exportMethods(sigmoid)
 exportMethods(sv)
 exportMethods(vonB)
 exportMethods(wt2len)
-import(plyr)
-import(reshape)
 import(FLCore)
 import(methods)
-importFrom(FLBRP, refpts, "refpts<-", brp, "fbar<-", FLBRP)
+importFrom(FLBRP,refpts)
 importFrom(methods,is)
+importFrom(plyr,.)
+importFrom(plyr,ddply)
 importFrom(popbio,lambda)

R/Rmd/lhPar.R

@@ -21,7 +21,7 @@
 #' 
 #' @export
 #' 
-#' @seealso \code{\link{r}}, \code{\link{loptAge}}, \code{\link{lhRef}}, \code{\link{lhPar}}, \code{\link{lhEql}}
+#' @seealso \code{\link{loptAge}}, \code{\link{lhRef}}, \code{\link{lhPar}}, \code{\link{lhEql}}
 #' 
 #' @import methods
 #' @docType methods

R/data.R

@@ -41,4 +41,32 @@ NULL
 #' }
 #' @name teleost
 #' 
+NULL
+
+#' wklife
+#'
+#' A dataset containing life history parameters for a range of teleost species
+#' 
+#' @docType data
+#' 
+#' @seealso \code{\link{teleost}}
+#' 
+#' @format A data frame with 15 rows (i.e. species) and 13 variables:
+#' \describe{
+#'   \item{species}{} 
+#'   \item{name}{} 
+#'   \item{area}{} 
+#'   \item{stock}{} 
+#'   \item{sex}{} 
+#'   \item{a}{scaling factor of the length weight relationship}       
+#'   \item{b}{exponent of the length weight relationship}       
+#'   \item{linf}{asymptotic length of the Von Bertalanffy growth equation}    
+#'   \item{k}{rate at which length reaches linf}       
+#'   \item{t0}{adjusts the growth equation for the initial size at birth}      
+#'   \item{lmax}{asymptotic length of the Von Bertalanffy growth equation}    
+#'   \item{l50}{length at which 50\% are mature}     
+#'   \item{a50}{age at which 50\% are mature}     
+#' }
+#' @name wklife
+#' 
 NULL

R/elasticity.R

@@ -127,7 +127,7 @@ doIt=function(what,par,dynamic=FALSE,fbar=FLQuant(c(seq(0,.75,length.out=21),seq
     par["M2"] =-par["M2"]
     units(par)=unt  
 
-    res=lh(par)
+    res=lhEql(par)
 
     fbar(res)=fbar
     res      =brp(res)
@@ -175,7 +175,7 @@ cvIt=function(what,par,dynamic=FALSE,fbar=FLQuant(c(seq(0,.75,length.out=21),seq
   func=function(x,par,fbar,dynamic=TRUE,what) {
 
     par[] =x
-    res=lh(par)
+    res=lhEql(par)
 
     fbar(res)=fbar
     res      =brp(res)

R/generic.R

@@ -5,7 +5,7 @@ utils::globalVariables(c("rbind.fill","data","FLBRP2biodyn","quantity","optimise
   "dmns","rho","stk","aaply","maply","alply","laply","error",
   "%^%","%*%","%-%","%+%","pow",
   "FLPar",
-  "lh","fbar<-","FLBRP","brp","refpts","refpts<-","as",
+  "fbar<-","FLBRP","brp","refpts","refpts<-","as",
   "computeRefpts","computeRefpts","catch.obs",
   "fwdWindow","aaply","invGascuelFn","laply","lambda",
   "asym","ddply",".","year","a","b","grad","ddply",".","x",'aaply',"invgompertzFn",

R/grw-dd.R

@@ -29,6 +29,7 @@
 #' @param params an \code{FLPar} with two values; i.e. a equal to M at unit mass and b a power term; defaults are a=0.3 and b=-0.288
 #' @param scale reference 
 #' @param k rate of change in density dependence
+#' @param fn function with growth model, with args age params
 #' @param ... other arguments, such as scale, e.g. stock numbers now relative to a reference level, e.g. at virgin biomass and k steepness of relationship
 #' 
 #' @aliases grwdd grwdd-method grwdd,FLQuant,FLPar-method

R/len-index.R

@@ -1,25 +1,20 @@
-# fn: no visible global function definition for ‘rmvnorm’
-# fn: no visible binding for global variable ‘bin’
-# fn: no visible binding for global variable ‘V1’
-# ldex: no visible binding for global variable ‘bin’
-# ldex: no visible binding for global variable ‘p’
-# mseEMP: no visible binding for global variable ‘mp’
-# mseSBT1: no visible binding for global variable ‘mp’
-# power : <anonymous>: no visible global function definition for
-# ‘powertrend’
-# power : <anonymous>: no visible binding for global variable ‘R’
-# power : <anonymous>: no visible binding for global variable ‘yrs’
-# power: no visible binding for global variable ‘pse’
-# power: no visible binding for global variable ‘increase’
-# power : <anonymous>: no visible global function definition for
-# ‘interpp’
-# refs,FLStock : <anonymous>: no visible binding for global variable
-# ‘regime’
-# refs,FLStock: no visible binding for global variable ‘b.msy’
-# refs,FLStock: no visible binding for global variable ‘b.current’
-# spectra,FLStock: no visible global function definition for ‘spectraFLQ’
-# Undefined global functions or variables:
-
+utils::globalVariables(c("rmvnorm"))
+utils::globalVariables(c("bin"))
+utils::globalVariables(c("V1"))
+utils::globalVariables(c("bin"))
+utils::globalVariables(c("p"))
+utils::globalVariables(c("mp"))
+utils::globalVariables(c("mp"))
+utils::globalVariables(c("powertrend"))
+utils::globalVariables(c("R"))
+utils::globalVariables(c("yrs"))
+utils::globalVariables(c("pse"))
+utils::globalVariables(c("increase"))
+utils::globalVariables(c("interpp"))
+utils::globalVariables(c("regime"))
+utils::globalVariables(c("b.msy"))
+utils::globalVariables(c("b.current"))
+utils::globalVariables(c("spectraFLQ"))
 
 fn=function(year,object,sigma,nsample=100) {
   n  =as.data.frame(stock.n(object)[,year]^(1/3),drop=TRUE)
@@ -36,6 +31,8 @@ fn=function(year,object,sigma,nsample=100) {
   idx =transform(idx,p=V1/sum(V1))
   idx}
 
+utils::globalVariables(c("adply"))
+
 fn2<-function(object,cv=0.3,nsample=100){
 
   sigma=matrix(0, ncol=dim(m(object))[1],nrow=dim(m(object))[1])

R/leslie.R

@@ -8,15 +8,15 @@
 #' @param numbers \code{boolean} numbers or biomass, numbers bt default
 #' @param ... any other arguments
 #' 
-#' @aliases leslie-method leslie,FLBRP-method
+#' @aliases leslie leslie-method leslie,FLBRP-method
 #' 
 #' @return \code{matrix}  
 #' 
 #' @export
 #' @docType methods
 #' @rdname leslie
 #' 
-#' @seealso \code{\link{r}}, \code{\link{lhRef}}, \code{\link{lhPar}}, \code{\link{lhEql}}
+#' @seealso \code{\link{lhRef}}, \code{\link{lhPar}}, \code{\link{lhEql}}
 #'  
 #' 
 #' @examples

R/lhPar.R

@@ -1,3 +1,8 @@
+utils::globalVariables(c("dlply"))
+utils::globalVariables(c("mlply"))
+utils::globalVariables(c("cast"))
+
+
 #' @title Generates life history parameters
 #' 
 #' @description 
@@ -21,7 +26,7 @@
 #' 
 #' @export
 #' 
-#' @seealso \code{\link{r}}, \code{\link{loptAge}}, \code{\link{lhRef}}, \code{\link{lhPar}}, \code{\link{lhEql}}
+#' @seealso \code{\link{loptAge}}, \code{\link{lhRef}}, \code{\link{lhPar}}, \code{\link{lhEql}}
 #' 
 #' @import methods
 #' @docType methods

R/lhRef.R

@@ -153,9 +153,9 @@ tmp=d_ply(scen,.(juve,dome,steep,m,species), with, {
   p["sr",]=ifelse(dome,5,5000)
 
   if (m=="Gislason"){
-    eql=lh(p)
+    eql=lhEql(p)
   }else{
-    eql=lh(p,m=function(params,length){
+    eql=lhEql(p,m=function(params,length){
       length[]=params["l50"]
       0.55*(length^-1.66)%*%(params["linf"]^1.44)%*%params["k"]})}
 

R/lopt.R

@@ -40,7 +40,7 @@ utils::globalVariables("growth")
 setMethod("lopt", signature(params="FLPar"),
        function(params,
                 m=function(length,params) exp(0.55)*(length^-1.61)%*%(params["linf"]^1.44)%*%params["k"],
-                growth=FLife:::vonB,
+                growth=vonB,
                 ...){   
             dmns=dimnames(params)
             dmns$params="lopt"

R/m-dd.R

@@ -25,14 +25,15 @@
 #'     
 #'    M=aL/(1+exp(-k(n-ref)))*wt^b;
 #'    
-#' @param wt  mass at which M is to be predicted
+#' @param object  mass at which M is to be predicted
 #' @param params an \code{FLPar} with two values; i.e. a equal to M at unit mass and b a power term; defaults are a=0.3 and b=-0.288
 #' @param scale reference 
 #' @param k rate of change in density dependence
-#' @param ... other arguments, such as scale, e.g. stock numbers now relative to a reference level, e.g. at virgin biomass and k steepness of relationship
+#' @param m function with mortality model, by default gisalson
 #' 
 #' @aliases mdd mdd-method mdd,FLQuant,FLPar-method
-#' 
+#' @param ... other arguments, such as scale, e.g. stock numbers now relative to a reference level, e.g. at virgin biomass and k steepness of relationship
+# 
 #' @export
 #' @docType methods
 #' @rdname mdd

R/mFn.R

@@ -15,7 +15,7 @@
 #'          jensen jensen-method jensen,FLPar-method
 #'          jensen2 jensen2-method jensen2,FLPar-method
 #'          charnov charnov-method charnov,FLQuant,FLPar-method
-#'          petersen petersen-method petersen,FLPar-method
+#'          petersen petersen-method petersen,FLPar-method petersen,FLQuant,FLPar-method
 #'          
 #' @return returns an object of \code{FLQuant}
 #' 
@@ -55,7 +55,7 @@
 #' 
 #' Varing by length, weight or age
 #' 
-#' @seealso \code{\link{gislason}},  \code{\link{lorenzen}}, \code{\link{chen}}
+#' @seealso \code{\link{gislason}},  \code{\link{lorenzen}}
 #' 
 #' @examples
 #' \dontrun{

R/powh.R

@@ -80,7 +80,8 @@
 #'  \emph{ICLARM Conf. Proc}, pages 53--74, 1987.
 #'   
 #' @aliases powh-method powh,numeric,numeric-method
-#'  
+#' @importFrom plyr ddply .
+#' 
 #' @export
 #' @docType methods
 #' @rdname powh

R/refs.R

@@ -18,7 +18,8 @@
 #' the average recruitment. 
 #'
 #' @param object \code{FLStock} 
-#' 
+#' @param ... other arguments
+#' @aliases refs refs-method refs,FLStock-method
 #' @return \code{data.frame} 
 #' 
 #' @export

R/richards.R

@@ -7,7 +7,8 @@
 #' @param params \code{FLPar} object with parameters \code{linf}, \code{k} and \code{t0}
 #' @param ... other arguments
 #' 
-#' @aliases richards richards-method richards,FLPar,FLPar-method richards,FLQuant,FLPar-method richards,FLQuant,numeric-method richards,missing,FLPar-method richards,numeric,numeric-method
+#' @aliases richards richards-method richards,FLPar,FLPar-method richards,FLQuant,FLPar-method richards,FLQuant,numeric-method richards,missing,FLPar-method richards,numeric,numeric-method #'          richards numeric,FLPar-method    
+
 #' 
 #' @return Returns an object of same class as \code{age}  e.g. \code{FLQuant}
 #' 

R/sbt-mse.R

@@ -164,7 +164,7 @@ if (FALSE){
   par=lhPar(FLPar(linf=100))  
   eql=lhEql(par)
   mou=as(eql,"FLStock")
-  mou=FLash::fwd(mou,f=fbar(eql)[,-1]/4,sr=eql)
+  mou=fwd(mou,f=fbar(eql)[,-1]/4,sr=eql)
 
   srDev=rlnorm(100,FLQuant(rep(0,136)),0.3)
 

R/spectra.R

@@ -1,3 +1,5 @@
+utils::globalVariables(c("adply"))
+
 setGeneric('spectra', function(object,...)  standardGeneric('spectra'))
 
 #Spectral analysis function

R/stars.R

@@ -1,5 +1,5 @@
 
-rodFn=function(data,year=NULL,plot=FALSE){
+rodFn<-function(data,year=NULL,plot=FALSE){
 
   if (is.null(year)) year=seq(length(data))
 

R/vonB.R

@@ -7,7 +7,7 @@
 #' @param params \code{FLPar} object with parameters \code{linf}, \code{k} and \code{t0}
 #' @param ... other arguments
 #' 
-#' @aliases vonB vonB-method vonB,FLPar,FLPar-method vonB,FLQuant,FLPar-method vonB,FLQuant,numeric-method vonB,missing,FLPar-method vonB,numeric,numeric-method
+#' @aliases vonB vonB-method vonB,FLPar,FLPar-method vonB,FLQuant,FLPar-method vonB,FLQuant,numeric-method vonB,missing,FLPar-method vonB,numeric,numeric-method vonB,numeric,FLPar-method
 #' 
 #' @return Returns an object of same class as \code{age}  e.g. \code{FLQuant}
 #'