some changes

R/MS_functions.R

@@ -673,9 +673,14 @@ Interim <- function(EM_out_dir = NULL, EM_init_dir = NULL,
 
     run_EM(EM_dir = EM_out_dir, verbose = verbose, check_converged = TRUE)
 
+    data_filename <- if(file.exists(file.path(OM_dir, "data.ss_new"))) {
+    "data.ss_new"
+      } else { 
+        "data_echo.ss_new"
+      }
 
     Reference_dat <- SS_readdat(
-      file = file.path(EM_out_dir, "data.ss_new"),
+      file = file.path(EM_out_dir, data_filename),
       version = 3.30, section = 2, verbose = FALSE
     )
 

R/develtools.R

@@ -28,7 +28,7 @@ test_no_par <- function(orig_mod_dir, new_mod_dir) {
   try(run_ss_model(new_mod_dir, "-maxfn 0 -phase 50 -nohess", verbose = FALSE))
   # read in the 2 par files.
   orig_par <- readLines(file.path(orig_mod_dir, "ss.par"))
-  if (file.exists(file.path(new_mod_dir, "data.ss_new"))) {
+  if (file.exists(file.path(new_mod_dir, "data.ss_new")) || file.exists(file.path(new_mod_dir, "data_echo.ss_new"))) {
     new_par <- readLines(file.path(new_mod_dir, "ss.par"))
     if (length(orig_par) != length(new_par)) {
       new_par_names <- grep("^# [^N]", new_par, value = TRUE)

R/initOM.R

@@ -384,12 +384,17 @@ create_OM <- function(OM_out_dir,
       )
     }
     # check model runs without producing nans in the data file
-    tmp_new_dat <- readLines(file.path(OM_out_dir, "data.ss_new"))
+    data_filepath <- if(file.exists(file.path(OM_out_dir, "data.ss_new"))) {
+      file.path(OM_out_dir, "data.ss_new")
+    } else  { 
+      file.path(OM_out_dir, "data_echo.ss_new")
+    }
+    tmp_new_dat <- readLines(data_filepath)
     nan_vals <- grep("nan", tmp_new_dat)
     if (length(nan_vals) > 0) {
       stop(
-        "NAN values present in the data.ss_new om file, suggesting an issue ",
-        "setting up the OM. See ", file.path(OM_out_dir, "data.ss_new")
+        "NAN values present in the ", basename(data_filepath)," om file, suggesting an issue ",
+        "setting up the OM. See ", data_filepath
       )
     }
 
@@ -487,14 +492,20 @@ run_OM <- function(OM_dir,
     debug_par_run = debug_par_run
   )
 
-  dat <- r4ss::SS_readdat(file.path(OM_dir, "data.ss_new"),
+  data_filename <- if(file.exists(file.path(OM_dir, "data.ss_new"))) {
+    "data.ss_new"
+  } else { 
+    "data_echo.ss_new"
+  }
+
+  dat <- r4ss::SS_readdat(file.path(OM_dir, data_filename),
     section = max_section,
     verbose = FALSE
   )
   # replace with the expected catch values if sample_catch is FALSE and using
   # bootstrap
   if (boot == TRUE & sample_catch == FALSE) {
-    exp_vals <- r4ss::SS_readdat(file.path(OM_dir, "data.ss_new"),
+    exp_vals <- r4ss::SS_readdat(file.path(OM_dir, data_filename),
       section = 2,
       verbose = FALSE
     )

R/results.R

@@ -139,10 +139,17 @@ plot_index_sampling <- function(dir = getwd()) {
     full.names = FALSE
   ), value = TRUE)
   assertive.types::assert_is_a_string(om_name)
+
+  data_file <- if(file.exists(file.path(dir, as.character(iters[1]), om_name, "data.ss_new"))){
+                  "data.ss_new"
+                  } else {
+                    "data_echo.ss_new"
+                    }
+
   tmp_dat_OM <- r4ss::SS_readdat(
     file.path(
       dir, as.character(iters[1]),
-      om_name, "data.ss_new"
+      om_name, data_file
     ),
     verbose = FALSE, section = 1
   )
@@ -154,7 +161,7 @@ plot_index_sampling <- function(dir = getwd()) {
   tmp_dat_OM <- r4ss::SS_readdat(
     file.path(
       dir, as.character(iters[1]),
-      om_name, "data.ss_new"
+      om_name, data_file
     ),
     verbose = FALSE, section = 2
   )

R/runSS.R

@@ -3,17 +3,17 @@
 
 #' Run an operating or estimation model
 #'
-#' This function takes care of calling SS. Importantly, it parses whether the
+#' This function takes care of calling SS3. Importantly, it parses whether the
 #' user is on Unix or Windows and calls the binary correctly. This lower-level
 #' function is meant to be called by higher level functions. Modified from
 #' run_ss3model in \href{https://github.com/ss3sim/ss3sim}{ss3sim}.
 #'
 #'
 #' @param dir The full or relative path to the model directory
-#' @param admb_options Any options to pass to SS command. Should be
+#' @param admb_options Any options to pass to SS3 command. Should be
 #'  of the form '-option'. Note that no checks are done to ensure this is a
 #'  valid ADMB command
-#' @param ss_bin Name of the SS executable. Defaults to "ss"
+#' @param ss3_bin Name of the SS3 executable. Defaults to "ss3"
 #' @param ignore.stdout Passed to \code{system}. If \code{TRUE} then ADMB
 #'   output is not printed on screen. This will be slightly faster. Set to
 #'  \code{FALSE} to help with debugging.
@@ -39,7 +39,7 @@
 #' @author Sean C. Anderson, Kathryn Doering
 run_ss_model <- function(dir,
                          admb_options = "",
-                         ss_bin = "ss",
+                         ss3_bin = "ss3",
                          ignore.stdout = TRUE,
                          admb_pause = 0.05,
                          show.output.on.console = FALSE,
@@ -53,15 +53,23 @@ run_ss_model <- function(dir,
   wd_orig <- getwd()
   on.exit(setwd(wd_orig))
   os <- .Platform[["OS.type"]]
-  bin <- get_bin(ss_bin)
+  bin <- get_bin(ss3_bin)
   if (check_run == TRUE) {
-    ss_new_path <- file.path(dir, "data.ss_new")
+    # new data file named for ss3 v.3.30.18 and prior
+    if(file.exists(file.path(dir, "data.ss_new"))) {
+      ss_new_path <- file.path(dir, "data.ss_new")
+    }
+    # new data file named for ss3 v.3.30.19 and after
+    if(file.exists(file.path(dir, "data_echo.ss_new"))) {
+      ss_new_path <- file.path(dir, "data_echo.ss_new")
+      }
+
     if (file.exists(ss_new_path)) {
       file.remove(ss_new_path)
     }
   }
 
-  if (verbose) message("Running SS.")
+  if (verbose) message("Running SS3.")
   if (os == "unix") {
     system(
       paste0(
@@ -88,7 +96,7 @@ run_ss_model <- function(dir,
       } else {
         stop(
           "data.ss_new was not created during the model run, which suggests ",
-          "SS did not run correctly"
+          "SS3 did not run correctly"
         )
       }
     } else {
@@ -104,8 +112,8 @@ run_ss_model <- function(dir,
 #' Get the binary/executable location in the package SSMSE. This function
 #' is from \href{https://github.com/ss3sim/ss3sim}{ss3sim}.
 #'
-#' @param bin_name Name of SS3 binary, defaults to "ss"
-#' @return The path to an SS binary. If using the GitHub version of the
+#' @param bin_name Name of SS3 binary, defaults to "ss3"
+#' @return The path to an SS3 binary. If using the GitHub version of the
 #'   package, this will be an internal binary. Otherwise, this function
 #'   will search for a version of the binary in your path. See the
 #'   ss3sim vignette.
@@ -114,7 +122,7 @@ run_ss_model <- function(dir,
 #' \dontrun{
 #' get_bin()
 #' }
-get_bin <- function(bin_name = "ss") {
+get_bin <- function(bin_name = "ss3") {
   # code inspiration from glmmADMB package:
   if (.Platform[["OS.type"]] == "windows") {
     platform <- "Windows64"
@@ -161,7 +169,7 @@ get_bin <- function(bin_name = "ss") {
     bin <- Sys.which(bin_name)[[1]]
     if (bin == "") {
       stop(
-        "The expected SS executable, ", bin_name, ", was not found in your",
+        "The expected SS3 executable, ", bin_name, ", was not found in your",
         " path. See the ss3sim vignette and ?ss3sim::run_ss3model for ",
         "instructions."
       )