new functions and revisions for reading input files from Neil Klaer

relates to issue #138 and #140, also incrementing package to 1.31.0

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: r4ss
 Type: Package
 Title: R Code for Stock Synthesis
-Version: 1.30.2
-Date: 2018-03-08
+Version: 1.31.0
+Date: 2018-05-09
 Author: Ian G. Taylor, Ian J. Stewart, Allan C. Hicks, Tommy M. Garrison,
     Andre E. Punt, John R. Wallace, Chantel R. Wetzel, James T. Thorson,
     Yukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C. Stawitz,
     Z. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L. Emmet,
     Sean C. Anderson, Gwladys I. Lambert, Megan M. Stachura,
-    Andrew B. Cooper, Andi Stephens, Neil Klaer, and Carey R. McGilliard
+    Andrew B. Cooper, Andi Stephens, Neil L. Klaer, and Carey R. McGilliard
 Maintainer: Ian G. Taylor <Ian.Taylor@noaa.gov>
 Depends:
     R (>= 2.10.0)

NAMESPACE

@@ -19,7 +19,10 @@ export(SS_profile)
 export(SS_read_summary)
 export(SS_readctl)
 export(SS_readctl_3.24)
+export(SS_readctl_3.30)
 export(SS_readdat)
+export(SS_readdat_2.00)
+export(SS_readdat_3.00)
 export(SS_readdat_3.24)
 export(SS_readdat_3.30)
 export(SS_readforecast)

R/SS_readctl.R

@@ -1,11 +1,11 @@
 #' read control file from SS
-#' 
+#'
 #' Read Stock Synthesis control file into list object in R. This function is a
 #' wrapper which calls either SS_readctl_3.24 or SS_readctl_3.30 (not yet written).
 #' This setup allows those functions to be cleaner (if somewhat redundant)
 #' than a single function that attempts to do everything.
-#' 
-#' 
+#'
+#'
 #' @param file Filename either with full path or relative to working directory.
 #' @param version SS version number. Currently only "3.24" or "3.30" are supported,
 #' either as character or numeric values (noting that numeric 3.30  = 3.3).
@@ -21,21 +21,24 @@
 #'  explicitly available in control file
 #' @param Ngenders number of genders in the model. This information is also not
 #'  explicitly available in control file
-#' @param Npopbins number of population bins in the model. This information is also not
-#'  explicitly available in control file and this information is only required if length based
+#' @param Npopbins number of population bins in the model. This information is
+#' also not explicitly available in control file and this information is only
+#' required if length based
 #'  maturity vector is directly supplied (Maturity option of 6), and not yet tested
 #' @param Nfleet number of fisheries in the model. This information is also not
 #'  explicitly available in control file
 #' @param Nsurveys number of survey fleets in the model. This information is also not
 #'  explicitly available in control file
-#' @param N_tag_groups number of tag release groups in the model. This information is also not
-#'  explicitly available in control file
-#' @author Ian G. Taylor, Yukio Takeuchi
+#' @param DatFile read datfile list for additional information for version 3.30
+#' and above
+#' @param N_tag_groups number of tag release groups in the model.
+#' This information is also not explicitly available in control file
+#' @author Ian G. Taylor, Yukio Takeuchi, Neil L Klaer
 #' @export
 #' @seealso \code{\link{SS_readctl_3.24}}, \code{\link{SS_readdat}},
 #' \code{\link{SS_readdat_3.24}}
 
-SS_readctl <- function(file, version="3.24", verbose=TRUE,echoall=FALSE,
+SS_readctl <- function(file, ctlversion="3.24", verbose=TRUE,echoall=FALSE,
                        ## Parameters that are not defined in control file
                        nseas=4,
                        N_areas=1,
@@ -44,16 +47,39 @@ SS_readctl <- function(file, version="3.24", verbose=TRUE,echoall=FALSE,
                        Npopbins=NA,
                        Nfleet=2,
                        Nsurveys=2,
-                       N_tag_groups=NA){
+                       DatFile=NA,
+                       N_tag_groups=NA,
+                       N_CPUE_obs=NA){
 
   # wrapper function to call old or new version of SS_readctl
 
   # automatic testing of version number could be added here in the future
   # see SS_readdat for example attempt
-
+
+  nver=as.numeric(substring(ctlversion,1,4))
+
+  if(verbose) cat("Char version is ", ctlversion, "\n")
+  if(verbose) cat("Numeric version is ", nver, "\n")
+
+  # call function for SS version 2.00
+  if(nver<3){
+
+    stop("Function SS_readctl_2.00 has not been written yet")
+
+  }
+
+  # call function for SS version 3.00
+  if((nver>=3)&&(nver<3.2)){
+
+    stop("Function SS_readctl_3.00 has not been written yet")
+
+  }
+
   # call function for SS version 3.24
-  if(version=="3.24"){ # should work whether "version" is character or numeric
+  if((nver>=3.2)&&(nver<3.3)){
+
     ctllist <- SS_readctl_3.24(file         = file,
+                               ctlversion   = ctlversion,
                                verbose      = verbose,
                                echoall      = echoall,
                                nseas        = nseas,
@@ -63,12 +89,29 @@ SS_readctl <- function(file, version="3.24", verbose=TRUE,echoall=FALSE,
                                Npopbins     = Npopbins,
                                Nfleet       = Nfleet,
                                Nsurveys     = Nsurveys,
-                               N_tag_groups = N_tag_groups)
+                               N_tag_groups = N_tag_groups,
+                               N_CPUE_obs   = N_CPUE_obs)
+
   }
 
   # call function for SS version 3.30
-  if(version=="3.30" | version==3.3){ # turns out 3.30 != "3.30" in R
-    stop("Function SS_readctl_3.30 has not been written yet")
+  if(nver>=3.3){
+
+    ctllist <- SS_readctl_3.30(file         = file,
+                               ctlversion   = ctlversion,
+                               verbose      = verbose,
+                               echoall      = echoall,
+                               nseas        = nseas,
+                               N_areas      = N_areas,
+                               Nages        = Nages,
+                               Ngenders     = Ngenders,
+                               Npopbins     = Npopbins,
+                               Nfleet       = Nfleet,
+                               Nsurveys     = Nsurveys,
+                               DatFile      = DatFile,
+                               N_tag_groups = N_tag_groups,
+                               N_CPUE_obs   = N_CPUE_obs)
+
   }
 
   # return the result