Roxygenizing FLCore

R/FLArray.R

@@ -88,6 +88,7 @@ setMethod("quant<-", signature(object="FLArray", value='character'),
 ) # }}}
 
 #  [             {{{
+
 #' Extract
 #'
 #' Extract or replace parts of an FLR Object
@@ -106,6 +107,10 @@ setMethod("quant<-", signature(object="FLArray", value='character'),
 #' Classes that are derived from \code{FLlst} (for example, \code{FLStocks} and
 #' \code{FLBiols}) can be subset in a similar way to ordinary list objects.
 #'
+#' '$' for the \code{FLPar} and \code{FLQuant} classes operate only along the first
+#' dimension ('params' or 'quant'), and are provided to be used specially in
+#' formulas.
+#'
 #' @name Extract
 #' @rdname Extract
 #' @aliases [,FLArray,ANY,ANY,ANY-method

R/FLComp.R

@@ -223,6 +223,8 @@ setMethod("units<-", signature(x="FLComp", value="list"),
 ) # }}}
 
 # '['       {{{
+#' @rdname Extract
+#' @aliases [,FLComp,ANY,ANY,ANY-method
 setMethod('[', signature(x='FLComp'),
 	function(x, i, j, k, l, m, n, ..., drop=FALSE) {
 
@@ -261,6 +263,8 @@ setMethod('[', signature(x='FLComp'),
 )   # }}}
 
 # "[<-"            {{{
+#' @rdname Extract
+#' @aliases [<-,FLComp,ANY,ANY,ANY-method
 setMethod("[<-", signature(x="FLComp"),
 	function(x, i, j, k, l, m, n, ..., value="missing")
   {

R/FLI.R

@@ -14,7 +14,9 @@ setMethod(computeCatch, signature("FLI"), function(object){
 })  # }}}
 
 # '['       {{{
-setMethod('[', signature(x='FLI'),
+#' @rdname Extract
+#' @aliases [,FLI,ANY,ANY,ANY-method
+setMethod('[', signature(x='FLI', i='ANY', j='ANY', drop='ANY'),
 	function(x, i, j, k, l, m, n, ..., drop=FALSE)
   {
 		qnames <- names(getSlots(class(x))[getSlots(class(x))=="FLQuant"])

R/FLIndexBiomass.R

@@ -10,6 +10,9 @@
 invisible(createFLAccesors("FLIndexBiomass", exclude=c('name', 'desc', 'range', 'effort'))) # }}}
 
 # FLIndexBiomass()   {{{
+
+#' @rdname FLIndexBiomass
+#' @aliases FLIndexBiomass,FLQuant-method
 setMethod('FLIndexBiomass', signature(object='FLQuant'),
   function(object, plusgroup=dims(object)$max, ...)
   {
@@ -37,6 +40,8 @@ setMethod('FLIndexBiomass', signature(object='FLQuant'),
   }
 )
 
+#' @rdname FLIndexBiomass
+#' @aliases FLIndexBiomass,missing-method
 setMethod('FLIndexBiomass', signature(object='missing'),
   function(...)
   {

R/FLPar.R

@@ -130,6 +130,8 @@ setMethod('FLPar', signature('FLPar'),
 ) # }}}
 
 # '['   {{{
+#' @rdname Extract
+#' @aliases [,FLPar,ANY,ANY,ANY-method
 setMethod('[', signature(x='FLPar'),
   function(x, i, j, k, l, m, n, ..., drop=FALSE) {
 
@@ -168,13 +170,17 @@ setMethod('[', signature(x='FLPar'),
   }
 )
 
-setMethod('[', signature(x='FLPar', i='array'),
-  function(x, i, ..., drop=FALSE) {
+#' @rdname Extract
+#' @aliases [,FLPar,array,missing,missing-method
+setMethod('[', signature(x='FLPar', i='array', j='missing', drop='missing'),
+  function(x, i) {
     return(x@.Data[i])
   }
 ) # }}}
 
 # "[<-"     {{{
+#' @rdname Extract
+#' @aliases [<-,FLPar,ANY,ANY,ANY-method
 setMethod("[<-", signature(x="FLPar", value="ANY"),
   function(x, i, j, k, l, m, n, ..., value)
   {
@@ -863,6 +869,8 @@ setMethod("model.frame", signature(formula="FLPar"),
 ) # }}}
 
 # $ {{{
+#' @rdname Extract
+#' @aliases $,FLPar-method
 setMethod('$', signature(x='FLPar'),
   function(x, name) {
     return(x[name,])

R/FLQuant.R

@@ -493,6 +493,9 @@ setMethod('yearTotals', signature(x='FLQuant'),
 ) # }}}
 
 # sums         {{{
+
+#' @rdname dimSummaries
+#' @aliases quantSums,FLQuant-method
 setMethod('quantSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
 
   res <- colSums(x, na.rm=na.rm)
@@ -509,18 +512,24 @@ setMethod('quantSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
     quant=quant(x), units=units(x)))
 })
 
+#' @rdname dimSummaries
+#' @aliases yearSums,FLQuant-method
 setMethod('yearSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
   return(apply(x,c(1,3,4,5,6), function(x, NA.RM=na.rm){
     z <- x[!is.na(x)]; ifelse(length(z), sum(z, na.rm=NA.RM), NA)
   }))
 })
 
+#' @rdname dimSummaries
+#' @aliases unitSums,FLQuant-method
 setMethod('unitSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
   return(apply(x,c(1,2,4,5,6), function(x, NA.RM=na.rm){
     z <- x[!is.na(x)]; ifelse(length(z), sum(z, na.rm=NA.RM), NA)
   }))
 })
 
+#' @rdname dimSummaries
+#' @aliases seasonSums,FLQuant-method
 setMethod('seasonSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
 
   # output, 1 season
@@ -541,6 +550,8 @@ setMethod('seasonSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
   return(res)
 })
 
+#' @rdname dimSummaries
+#' @aliases areaSums,FLQuant-method
 setMethod('areaSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
   return(apply(x,c(1,2,3,4,6), function(x, NA.RM=na.rm){
     z <- x[!is.na(x)]; ifelse(length(z), sum(z, na.rm=NA.RM), NA)
@@ -1187,6 +1198,8 @@ setMethod("tsp", signature(x="FLQuant"),
 ) # }}}
 
 # $ {{{
+#' @rdname Extract
+#' @aliases $,FLQuant-method
 setMethod("$", signature(x="FLQuant"),           
   function(x, name) {
     return(x[name,])

R/FLQuantDistr.R

@@ -199,6 +199,8 @@ setMethod("-",
 ) # }}}
 
 ## "["             {{{
+#' @rdname Extract
+#' @aliases [,FLQuantDistr,ANY,ANY,ANY-method
 setMethod("[", signature(x="FLQuantDistr"),
     function(x, i, j, k, l, m, n) {
 
@@ -227,6 +229,8 @@ setMethod("[", signature(x="FLQuantDistr"),
 	}
 ) 
 
+#' @rdname Extract
+#' @aliases [,FLQuantDistr,array,missing,missing-method
 setMethod("[", signature(x="FLQuantDistr", i="array", j="missing", drop="missing"),
   function(x, i)
   {

R/FLSR.R

@@ -17,7 +17,26 @@
 #' formulation implemented for each of them.
 #'
 #' @name FLSR
-#' @aliases FLSR-class FLSR FLSR-methods FLSR,ANY-method FLSR,missing-method
+#' @aliases FLSR-class covar,FLSR-method desc,FLSR-method details,FLSR-method
+#' distribution,FLSR-method fitted,FLSR-method gr,FLSR-method
+#' hessian,FLSR-method initial,FLSR-method logl,FLSR-method
+#' logLik,FLSR-method model,FLSR-method name,FLSR-method
+#' params,FLSR-method range,FLSR-method rec,FLSR-method
+#' residuals,FLSR-method ssb,FLSR-method vcov,FLSR-method
+#' covar<-,FLSR,FLQuants-method desc<-,FLSR,character-method
+#' details<-,FLSR,list-method distribution<-,FLSR,character-method
+#' distribution<-,FLSR,factor-method fitted<-,FLSR,FLArray-method
+#' fitted<-,FLSR,numeric-method gr<-,FLSR,function-method
+#' hessian<-,FLSR,array-method initial<-,FLSR,function-method
+#' logl<-,FLSR,function-method logLik<-,FLSR,logLik-method
+#' logLik<-,FLSR,numeric-method model<-,FLSR,character-method
+#' model<-,FLSR,formula-method model<-,FLSR,function-method
+#' model<-,FLSR,list-method name<-,FLSR,character-method
+#' params<-,FLSR,FLPar-method range<-,FLSR,numeric-method
+#' rec<-,FLSR,FLQuant-method rec<-,FLSR,numeric-method
+#' residuals<-,FLSR,FLArray-method residuals<-,FLSR,numeric-method
+#' ssb<-,FLSR,FLQuant-method ssb<-,FLSR,numeric-method
+#' vcov<-,FLSR,array-method
 #' @docType class
 #' @section Slots: \describe{
 #'     \item{name}{Name of the object (\code{character}).}
@@ -129,6 +148,8 @@ setClass('FLSR',
 invisible(createFLAccesors("FLSR", include=c('rec', 'ssb', 'covar'))) # }}}
 
 # FLSR()	{{{
+#' @rdname FLSR
+#' @aliases FLSR,ANY-method
 setMethod('FLSR', signature(model='ANY'),
   function(model, ...)
   {
@@ -164,6 +185,8 @@ setMethod('FLSR', signature(model='ANY'),
     return(res)
   }
 )
+#' @rdname FLSR
+#' @aliases FLSR,missing-method
 setMethod('FLSR', signature(model='missing'),
 	function(...)
 		return(FLSR(formula(NULL), ...))) # }}}
@@ -383,12 +406,15 @@ setClass("FLSRs", contains="FLComps",
   }
 )
 
-# constructor
+#' @rdname FLSRs
+#' @aliases FLSRs,FLSR-method
 setMethod("FLSRs", signature(object="FLSR"), function(object, ...) {
     lst <- c(object, list(...))
     FLSRs(lst)
 })
 
+#' @rdname FLSRs
+#' @aliases FLSRs,missing-method
 setMethod("FLSRs", signature(object="missing"),
   function(...) {
     # empty
@@ -404,6 +430,8 @@ setMethod("FLSRs", signature(object="missing"),
   }
 )
 
+#' @rdname FLSRs
+#' @aliases FLSRs,list-method
 setMethod("FLSRs", signature(object="list"),
   function(object, ...) {
 

R/FLStock.R

@@ -5,8 +5,9 @@
 # Maintainer: Iago Mosqueira, EC JRC
 
 # FLStock()   {{{
+
 #' @rdname FLStock
-#' @aliases FLStock,FLQuant-method FLStock,missing-method
+#' @aliases FLStock,FLQuant-method
 setMethod('FLStock', signature(object='FLQuant'),
   function(object, plusgroup=dims(object)$max, ...) {
 
@@ -42,6 +43,8 @@ setMethod('FLStock', signature(object='FLQuant'),
   }
 )
 
+#' @rdname FLStock
+#' @aliases FLStock,missing-method
 setMethod('FLStock', signature(object='missing'),
   function(...)
   {
@@ -74,6 +77,8 @@ setMethod('FLStock', signature(object='missing'),
   }
 )
 
+#' @rdname FLStock
+#' @aliases FLStock,FLQuants-method
 setMethod('FLStock', signature(object='FLQuants'),
   function(object, ...)
   {
@@ -473,6 +478,8 @@ setMethod("ssbpurec",signature(object="FLStock"),
 )# }}}
 
 # '['       {{{
+#' @rdname Extract
+#' @aliases [,FLStock,ANY,ANY,ANY-method
 setMethod('[', signature(x='FLStock'),
 	function(x, i, j, k, l, m, n, ..., drop=FALSE)
   {
@@ -517,6 +524,8 @@ setMethod('[', signature(x='FLStock'),
 )   # }}}
 
 # "[<-"            {{{
+#' @rdname Extract
+#' @aliases [<-,FLStock,ANY,ANY,FLStock-method
 setMethod("[<-", signature(x="FLStock", value="FLStock"),
 	function(x, i, j, k, l, m, n, ..., value) {
     if (missing(i))

R/FLlst-methods.R

@@ -12,6 +12,9 @@ setAs("NULL", "FLQuant", function(from) FLQuant())
 # }}}
 
 # replacement, [[<-, $, [<- {{{
+
+#' @rdname Extract
+#' @aliases [[<-,FLlst,ANY,missing,ANY-method
 setReplaceMethod("[[", signature(x="FLlst", i="ANY", j="missing", value="ANY"),
 	function(x, i, j, value)
 	{
@@ -37,6 +40,8 @@ setReplaceMethod("[[", signature(x="FLlst", i="ANY", j="missing", value="ANY"),
 	}
 )
 
+#' @rdname Extract
+#' @aliases $<-,FLlst,ANY-method
 setReplaceMethod("$", signature(x="FLlst", value="ANY"),
 	function(x, name, value)
 	{
@@ -64,6 +69,8 @@ setReplaceMethod("$", signature(x="FLlst", value="ANY"),
 			stop("Invalid object, classes do not match.")
 })
 
+#' @rdname Extract
+#' @aliases [<-,FLlst,ANY,missing,ANY-method
 setReplaceMethod("[", signature(x="FLlst", i="ANY", j="missing", value="ANY"),
 	function(x, i, j, value)
 	{
@@ -87,15 +94,16 @@ setReplaceMethod("[", signature(x="FLlst", i="ANY", j="missing", value="ANY"),
 	}
 ) # }}}
 
-# subset, [ {{{
-
-
-setMethod("[", signature(x="FLlst", i="ANY", j="missing", drop="ANY"), function(x,i,j,drop){
-	lst <- as(x, "list")
-  # names dropped!
-  names(lst) <- names(x)
-	lst <- lst[i]
-	new(is(x), lst)
+# [ {{{
+#' @rdname Extract
+#' @aliases [,FLlst,ANY,missing,ANY-method
+setMethod("[", signature(x="FLlst", i="ANY", j="missing", drop="ANY"),
+  function(x,i,j,drop){
+	  lst <- as(x, "list")
+    # names dropped!
+    names(lst) <- names(x)
+	  lst <- lst[i]
+	  new(is(x), lst)
 })  # }}}
 
 # lapply  {{{