Deprecate 3.24 functions

R/SS_changepars.R

@@ -331,7 +331,7 @@ SS_changepars <-
     if (verbose) {
       message(
         "Wrote new file to ", newctlfile, " with the following changes:\n",
-        paste0(capture.output(results), collapse = "\n")
+        paste0(utils::capture.output(results), collapse = "\n")
       )
     }
     return(invisible(results))

R/SS_fitbiasramp.R

@@ -322,7 +322,7 @@ SS_fitbiasramp <-
         warning("Problem with convergence, here is output from 'optim':\n")
         print(newbias)
       }
-      message("Estimated values: \n", paste0(capture.output(df), collpase = "\n"))
+      message("Estimated values: \n", paste0(utils::capture.output(df), collpase = "\n"))
     }
 
     if (plot) {

R/SS_readctl_3.24.R

@@ -1,11 +1,12 @@
-#' read control file from SS version 3.24
+#' Deprecated: read control file from SS version 3.24
 #'
 #' Read Stock Synthesis (version 3.24) control file into list object in R.
 #' This function comes with its wrapper function SS_readctl
 #' that calls SS_readctl_3.24 (this function) or SS_readctl_3.30
-#' (to be available in future).
-#'
 #'
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
+#' 
 #' @template file
 #' @template verbose
 #' @template readctl_vars
@@ -46,6 +47,12 @@ SS_readctl_3.24 <- function(file,
                             N_CPUE_obs = NULL,
                             ##################################
                             ptype = lifecycle::deprecated()) {
+  # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_readctl_3.24()",
+    details = "Please update model to version 3.30."
+  )
   # deprecated variable warnings -----
   # soft deprecated for now, but fully deprecate in the future.
   if (lifecycle::is_present(ptype)) {

R/SS_readdat_2.00.R

@@ -1,10 +1,12 @@
-#' read data file from SS version 2.00
+#' Deprecated: read data file from SS version 2.00
 #'
 #' Read Stock Synthesis (version 2.00) data file into list object in R.
 #' This function was formerly called SS_readdat. That name is now used
 #' for a wrapper function that calls either SS_readdat_2.00 SS_readdat_3.00
 #' SS_readdat_3.24 or SS_readdat_3.30 (and potentially additional functions in the future).
 #'
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
 #'
 #' @template file
 #' @template verbose
@@ -21,6 +23,12 @@
 #' [SS_writeforecast()], [SS_writedat()]
 SS_readdat_2.00 <- function(file, verbose = TRUE,
                             echoall = lifecycle::deprecated(), section = NULL) {
+  # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_readdat_2.00()",
+    details = "Please update model to version 3.30."
+  )
   # function to read Stock Synthesis data files
   if (lifecycle::is_present(echoall)) {
     lifecycle::deprecate_warn(
@@ -146,7 +154,7 @@ SS_readdat_2.00 <- function(file, verbose = TRUE,
   areas <- datlist[["areas"]]
   if (verbose) {
     message("areas:", areas)
-    message("fleet info:\n", paste0(capture.output(
+    message("fleet info:\n", paste0(utils::capture.output(
       data.frame(
         fleet = 1:Ntypes,
         name = fleetnames,

R/SS_readdat_3.00.R

@@ -1,10 +1,13 @@
-#' read data file from SS version 3.00
+#' Deprecate: read data file from SS version 3.00
 #'
 #' Read Stock Synthesis (version 3.00) data file into list object in R.
 #' This function was formerly called SS_readdat. That name is now used
 #' for a wrapper function that calls either SS_readdat_3.24 or SS_readdat_3.30
 #' (and potentially additional functions in the future).
 #'
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
+#'
 #'
 #' @template file
 #' @template verbose
@@ -21,6 +24,12 @@
 #' [SS_writeforecast()], [SS_writedat()]
 SS_readdat_3.00 <- function(file, verbose = TRUE,
                             echoall = lifecycle::deprecated(), section = NULL) {
+                                # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_readdat_3.00()",
+    details = "Please update model to version 3.30."
+  )
   # function to read Stock Synthesis data files
   if (lifecycle::is_present(echoall)) {
     lifecycle::deprecate_warn(
@@ -140,7 +149,7 @@ SS_readdat_3.00 <- function(file, verbose = TRUE,
   i <- i + Ntypes
   if (verbose) {
     message("areas:", areas)
-    message("fleet info:\n", paste0(capture.output(
+    message("fleet info:\n", paste0(utils::capture.output(
       data.frame(
         fleet = 1:Ntypes,
         name = fleetnames,

R/SS_readdat_3.24.R

@@ -1,10 +1,9 @@
-#' read data file from SS version 3.24
+#' Deprecated: read data file from SS version 3.24
 #'
 #' Read Stock Synthesis (version 3.24) data file into list object in R.
-#' This function was formerly called SS_readdat. That name is now used
-#' for a wrapper function that calls either SS_readdat_3.24 or SS_readdat_3.30
-#' (and potentially additional functions in the future).
-#'
+#' 
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
 #'
 #' @template file
 #' @template verbose
@@ -21,7 +20,12 @@
 #' [SS_writestarter()],
 #' [SS_writeforecast()], [SS_writedat()]
 SS_readdat_3.24 <- function(file, verbose = TRUE, echoall = lifecycle::deprecated(), section = NULL) {
-
+  # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_readdat_3.24()",
+    details = "Please update model to version 3.30."
+  )
   # deprecated arguments
   if (lifecycle::is_present(echoall)) {
     lifecycle::deprecate_warn(
@@ -138,7 +142,7 @@ SS_readdat_3.24 <- function(file, verbose = TRUE, echoall = lifecycle::deprecate
   i <- i + Ntypes
   if (verbose) {
     message("areas:", areas)
-    message("fleet info:\n", paste0(capture.output(
+    message("fleet info:\n", paste0(utils::capture.output(
       data.frame(
         fleet = 1:Ntypes,
         name = fleetnames,

R/SS_readpar_3.24.R

@@ -1,7 +1,9 @@
-#' read ss.par file from SS version 3.24
+#' Deprecated: read ss.par file from SS version 3.24
 #'
 #' Read Stock Synthesis (version 3.24) parameter file into list object in R.
 #'
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
 #'
 #' @param parfile Filename either with full path or relative to working directory.
 #' @param datsource list or character. If list, should be a list produced
@@ -20,6 +22,12 @@
 #' [SS_writestarter()],
 #' [SS_writeforecast()], [SS_writedat()]
 SS_readpar_3.24 <- function(parfile, datsource, ctlsource, verbose = TRUE) {
+  # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_readpar_3.24()",
+    details = "Please update model to version 3.30."
+  )
   if (is.character(datsource)) {
     datlist <- SS_readdat(file = datsource, version = "3.24", verbose = FALSE)
   } else if (is.list(datsource)) {

R/SS_varadjust.R

@@ -145,7 +145,7 @@ SS_varadjust <- function(dir = "C:/myfiles/mymodels/myrun/",
   if (verbose) {
     message(
       "Existing table of variance adjustments:\n",
-      paste0(capture.output(ctl), collapse = "\n")
+      paste0(utils::capture.output(ctl), collapse = "\n")
     )
   }
 
@@ -176,7 +176,7 @@ SS_varadjust <- function(dir = "C:/myfiles/mymodels/myrun/",
   if (verbose) {
     message(
       "New table of variance adjustments:\n",
-      paste0(capture.output(ctl), collapse = "\n")
+      paste0(utils::capture.output(ctl), collapse = "\n")
     )
   }
 

R/SS_writectl_3.24.R

@@ -1,7 +1,11 @@
-#' write control file
+#' Deprecated: write 3.24 control file
 #'
 #' write Stock Synthesis control file from list object in R which was probably
 #' created using [SS_readctl()]
+#' 
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
+#'
 #' @param ctllist  List object created by [SS_readctl()].
 #' @param outfile Filename for where to write new data file.
 #' @template overwrite
@@ -14,6 +18,12 @@
 # ' \code{\link{SS_writedat}}
 SS_writectl_3.24 <- function(ctllist, outfile, overwrite = FALSE,
                              verbose = FALSE) {
+                                # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_writectl_3.24()",
+    details = "Please update model to version 3.30."
+  )
   # Add msgs for deprecated args ----
   # these should be removed after 1 release version.
 

R/SS_writedat_3.24.R

@@ -1,10 +1,12 @@
-#' write data file for SS version 3.24
+#' Deprecated: write data file for SS version 3.24
 #'
 #' Write Stock Synthesis data file from list object in R which was probably
 #' created using [SS_readdat()] (which would have called on
 #' [SS_readdat_3.24()]).
 #'
-#'
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
+#' 
 #' @param datlist List object created by [SS_readdat()].
 #' @param outfile Filename for where to write new data file.
 #' @template overwrite
@@ -24,6 +26,12 @@ SS_writedat_3.24 <- function(datlist,
                              overwrite = FALSE,
                              faster = lifecycle::deprecated(),
                              verbose = TRUE) {
+                                # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_writedat_3.24()",
+    details = "Please update model to version 3.30."
+  )
   # function to write Stock Synthesis data files
   if (verbose) {
     message("running SS_writedat_3.24")

R/SS_writepar_3.24.R

@@ -1,7 +1,9 @@
-#' write ss.par file from SS version 3.24
+#' Deprecated: write ss.par file from SS version 3.24
 #'
 #' Write Stock Synthesis (version 3.24) parameter file from list object in R to file.
 #'
+#' Support for 3.24 models within the r4ss `SS_read*` and `SS_write*()`
+#' functions is ending, so please update models to 3.30. 
 #'
 #' @param parlist  List object created by [SS_readpar_3.24()].
 #' @param outfile Filename for where to write new parameter file.
@@ -16,7 +18,12 @@
 #' [SS_writestarter()],
 #' [SS_writeforecast()], [SS_writedat()]
 SS_writepar_3.24 <- function(parlist, outfile, overwrite = TRUE, verbose = FALSE) {
-
+  # deprecate. Remove code upon next release.
+  lifecycle::deprecate_warn(
+    when = "1.45.3",
+    what = "SS_writepar_3.24()",
+    details = "Please update model to version 3.30."
+  )
   # function to write Stock Synthesis parameter files
   if (verbose) message("running SS_writepar_3.24")
 

R/SSmakeMmatrix.R

@@ -109,7 +109,7 @@ SSmakeMmatrix <- function(mat, startyr, outfile = NULL,
 
   message(
     "Mortality params to paste into the first block of parameter lines:\n",
-    paste0(capture.output(Mparams), collapse = "\n")
+    paste0(utils::capture.output(Mparams), collapse = "\n")
   )
   printdf(Mparams)
 
@@ -134,7 +134,7 @@ SSmakeMmatrix <- function(mat, startyr, outfile = NULL,
   message(
     "\n# stuff to paste below the line labeled 'CohortGrowDev'\n",
     "1 #_custom mortality/growth environmental setup\n",
-    paste0(capture.output(Mlinks), collapse = "\n")
+    paste0(utils::capture.output(Mlinks), collapse = "\n")
   )
 
   # create a data frame of environmental variables
@@ -157,7 +157,7 @@ SSmakeMmatrix <- function(mat, startyr, outfile = NULL,
     "Environmental variables to paste into the bottom of the data file:\n",
     maxage + 1, " # N environmental variables\n",
     nrow(Menv), " # N environmental observations\n",
-    paste0(capture.output(Menv), collapse = "\n")
+    paste0(utils::capture.output(Menv), collapse = "\n")
   )
 
   # restore things to how they were

R/SSplotRecdist.R

@@ -86,7 +86,7 @@ SSplotRecdist <-
     colnames(recmat) <- seasnames
     message(
       "recruitment distribution by area and season:\n",
-      paste0(capture.output(recmat), collapse = "\n")
+      paste0(utils::capture.output(recmat), collapse = "\n")
     )
     if (plot) recdistfun()
     if (print) {