64 bit FLXSA, FLCoreClasses.cpp included in pkg

.Rbuildignore

@@ -4,3 +4,4 @@ man-roxygen/
 Makefile
 .git/
 ^appveyor\.yml$
+^_pkgdown.yml$

DESCRIPTION

@@ -3,12 +3,18 @@ Title: eXtended Survivor Analysis for FLR
 Authors@R: c(
   person("Iago", "Mosqueira", email = "iago.mosqueira@ec.europa.eu", role = "cre"),
   person("Laurence T.", "Kell", email = "laurie.kell@iccat.int", role = "aut"))
-Version: 2.6.0
-Date: 2017-09-18
-Description: Creates stock numbers at age from commercial catch data
+Version: 2.6.1
+Date: 2017-10-10
+Description:
+  Calculates stock numbers and fishing mortality at age from commercial
+  catch data and one or more indices of abundance suing the method in
+  Darby and Flatman (1994) and Shepherd (1999).
 License: GPL-2
 Depends:
-    FLCore(>= 2.5),
-    FLAssess(>= 2.5)
-LinksTo: FLash(>= 2.5)
+  methods,
+  FLCore(>= 2.6),
+  FLAssess(>= 2.5)
+Suggests:
+    testthat
+Additional_repositories: http://flr-project.org/R
 RoxygenNote: 6.0.1

NAMESPACE

@@ -1,17 +1,18 @@
-useDynLib("FLXSA")
+useDynLib("FLXSA", .registration = TRUE)
+import("methods")
 import("FLCore")
 import("FLAssess")
 exportClasses(
-    "FLXSA",
-    "FLXSA.control")
+  "FLXSA",
+  "FLXSA.control")
 export(
-    "FLXSA",
-    "FLXSA.control",
-  	"is.FLXSA",
-    "is.FLXSA.control")
+  "FLXSA",
+  "FLXSA.control",
+  "is.FLXSA",
+  "is.FLXSA.control")
 exportMethods(
-    "show",
-    "assess",
-    "diagnostics",
-		"rand",
-    "summary")
+  "show",
+  "assess",
+  "diagnostics",
+	"rand",
+  "summary")

R/FLXSA.R

@@ -232,15 +232,15 @@ setMethod("FLXSA", signature(stock="FLStock", indices="FLIndices"),
 
     if(!diag.flag) {
 
-      res<-.Call("FLXSA", iter(stock, 1), lapply(indices, iter, 1), control, FALSE)
+      res<-.Call("runFLXSA", iter(stock, 1), lapply(indices, iter, 1), control, FALSE)
       iters <- max(iters.stock,iters.indices)
 
       if (iters>1) {
 
         res@stock.n<-propagate(FLQuant(res@stock.n@.Data),iters)
         res@harvest<-propagate(FLQuant(res@harvest@.Data),iters)
         for (i in as.character(2:iters)) {
-          res. <- .Call("FLXSA", iter(stock,i), lapply(indices, iter,i), control, FALSE)
+          res. <- .Call("runFLXSA", iter(stock,i), lapply(indices, iter,i), control, FALSE)
           iter(res@stock.n,i)<-FLQuant(res.@stock.n@.Data)
           iter(res@harvest,i)<-FLQuant(res.@harvest@.Data)
         }
@@ -252,9 +252,7 @@ setMethod("FLXSA", signature(stock="FLStock", indices="FLIndices"),
       return(res)
       }
 
-    # res <-.Call("FLXSA", stock, indices, control, diag.flag)
-
-    res <-fqs(.Call("FLXSA", stock, indices, control, diag.flag))
+    res <-fqs(.Call("runFLXSA", stock, indices, control, diag.flag))
 
     if (class(res) != "FLXSA")
       return(res)
@@ -524,6 +522,7 @@ is.FLXSA <- function(x)
 	return(inherits(x, "FLXSA"))
 # }}}
 
+# is.FLXSA.control {{{
 # Test if an object is of FLXSA.control class
 is.FLXSA.control <- function(x)
 	return(inherits(x, "FLXSA.control"))
@@ -535,17 +534,9 @@ setMethod("show", signature(object="FLXSA.control"),
 	   for (i in 1:length(n.))
          cat(n.[i],"\t\t",slot(object,n.[i]),"\n")
 	}
-)
-
-
-# DiagsXSA::FLXSA
-# Author     : MP, KH & JJP, EJ
-# Modified to become summary fof FLXSA
-# Updated    : RDS   11/11/10 
-# ---------------------------------------------------------------------------------
-
-
+) # }}}
 
+# diagnostics {{{
 setGeneric("diagnostics", function(object, ...){
 	standardGeneric("diagnostics")
 	}
@@ -730,5 +721,4 @@ if(sections[8]){
 }
     invisible()
 }
-)
-
+) # }}}