more updates for v3.30.21; still not working yet though

R/MS_functions.R

@@ -673,11 +673,7 @@ 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"
-      }
+    data_filename <- list.files(file.path(OM_dir), pattern = "data.ss_new|data_echo.ss_new")
 
     Reference_dat <- SS_readdat(
       file = file.path(EM_out_dir, data_filename),

R/develop_OMs.R

@@ -104,6 +104,9 @@ develop_OMs <- function(OM_name = NULL, OM_in_dir = NULL, out_dir = getwd(), par
       if (!file.exists(file.path(tmp_mod_path, "control.ss_new"))) {
         warning("Problem refitting model in ", tmp_mod_path)
       }
+      if (file.exists(file.path(tmp_mod_path,"data.ss_new")) && file.exists(file.path(tmp_mod_path,"data_echo.ss_new"))) {
+        file.remove(file.path(tmp_mod_path,"data.ss_new"))
+      }
     } else {
       # run with no estimation
       run_ss_model(
@@ -114,6 +117,9 @@ develop_OMs <- function(OM_name = NULL, OM_in_dir = NULL, out_dir = getwd(), par
       if (!file.exists(file.path(tmp_mod_path, "control.ss_new"))) {
         warning("Problem running model without estimation in ", tmp_mod_path)
       }
+      if (file.exists(file.path(tmp_mod_path,"data.ss_new")) && file.exists(file.path(tmp_mod_path,"data_echo.ss_new"))) {
+        file.remove(file.path(tmp_mod_path,"data.ss_new"))
+      }
       # add back original recdevs into the model (b/c not specified through the ctl file)
       new_parfile <- r4ss::SS_readpar_3.30(
         parfile = file.path(tmp_mod_path, "ss.par"),

R/develtools.R

@@ -28,7 +28,10 @@ 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")) || file.exists(file.path(new_mod_dir, "data_echo.ss_new"))) {
+
+  dat_file <- list.files(file.path(new_mod_dir), pattern = "data.ss_new|data_echo.ss_new")
+
+  if (file.exists(file.path(new_mod_dir, dat_file))) {
     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)
@@ -49,7 +52,7 @@ test_no_par <- function(orig_mod_dir, new_mod_dir) {
       stop(
         "Problem with the ss.par file - same number of lines. ",
         "The original par file in ", orig_mod_dir,
-        " has the same number of values as the new ",
+        "has the same number of values as the new ",
         "par in ", new_mod_dir, ", so not sure what the issue is."
       )
     }

R/initOM.R

@@ -72,7 +72,7 @@ create_OM <- function(OM_out_dir,
   # read in files to use ----
   dat <- r4ss::SS_readdat(
     file = file.path(OM_out_dir, start[["datfile"]]),
-    verbose = FALSE, section = 1
+    verbose = FALSE
   )
   forelist <- r4ss::SS_readforecast(
     file = file.path(OM_out_dir, "forecast.ss"),
@@ -333,8 +333,6 @@ create_OM <- function(OM_out_dir,
     if (!is.null(dat[["age_info"]])) dat[["age_info"]][["mintailcomp"]] <- -1
   }
 
-
-
   # write all files
   r4ss::SS_writectl(
     ctllist = ctl, outfile = file.path(OM_out_dir, start[["ctlfile"]]),
@@ -365,6 +363,9 @@ create_OM <- function(OM_out_dir,
       verbose = verbose,
       debug_par_run = TRUE
     )
+    if (file.exists(file.path(OM_out_dir,"data.ss_new")) && file.exists(file.path(OM_out_dir,"data_echo.ss_new"))) {
+        file.remove(file.path(OM_out_dir,"data.ss_new"))
+      }
     # TODO: maybe add the following check into the debug par run arg of run_ss_model?
     check_par <- readLines(file.path(OM_out_dir, "ss.par"))
     check_sum_val <- check_par[grep("checksum999", check_par) + 1]
@@ -384,11 +385,7 @@ create_OM <- function(OM_out_dir,
       )
     }
     # check model runs without producing nans in the data file
-    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")
-    }
+    data_filepath <- list.files(file.path(OM_out_dir), pattern = "data.ss_new|data_echo.ss_new", full.names = TRUE)
     tmp_new_dat <- readLines(data_filepath)
     nan_vals <- grep("nan", tmp_new_dat)
     if (length(nan_vals) > 0) {
@@ -476,7 +473,7 @@ run_OM <- function(OM_dir,
   if (is.null(seed)) {
     seed <- stats::runif(1, 1, 9999999)
   }
-
+  # browser()
   start <- r4ss::SS_readstarter(file.path(OM_dir, "starter.ss"),
     verbose = FALSE
   )
@@ -491,13 +488,10 @@ run_OM <- function(OM_dir,
     verbose = verbose,
     debug_par_run = debug_par_run
   )
-
-  data_filename <- if(file.exists(file.path(OM_dir, "data.ss_new"))) {
-    "data.ss_new"
-  } else { 
-    "data_echo.ss_new"
-  }
-
+  if (file.exists(file.path(OM_dir,"data.ss_new")) && file.exists(file.path(OM_dir,"data_echo.ss_new"))) {
+        file.remove(file.path(OM_dir,"data.ss_new"))
+      }
+  data_filename <- list.files(file.path(OM_dir), pattern = "data.ss_new|data_echo.ss_new")
   dat <- r4ss::SS_readdat(file.path(OM_dir, data_filename),
     section = max_section,
     verbose = FALSE

R/results.R

@@ -140,12 +140,7 @@ plot_index_sampling <- function(dir = getwd()) {
   ), 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"
-                    }
-
+  data_file <- list.files(file.path(dir,as.character(iters[1]), om_name), pattern = "data.ss_new|data_echo.ss_new")
   tmp_dat_OM <- r4ss::SS_readdat(
     file.path(
       dir, as.character(iters[1]),
@@ -369,7 +364,8 @@ get_performance_metrics <- function(dir = getwd(),
           )
         }
         om_mod_path <- tmp_mods[om_mod]
-        dat <- r4ss::SS_readdat(file.path(om_mod_path, "data.ss_new"),
+        om_mod_dat <- list.files(file.path(om_mod_path), pattern = "data.ss_new|data_echo.ss_new")
+        dat <- r4ss::SS_readdat(file.path(om_mod_path, om_mod_dat),
           section = 1, verbose = FALSE
         )
         tmp_catch <- dat[["catch"]]

R/runSS.R

@@ -56,19 +56,16 @@ run_ss_model <- function(dir,
   bin <- get_bin(ss3_bin)
   if (check_run == TRUE) {
     # 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(file.path(dir,"data.ss_new")) && file.exists(file.path(dir,"data_echo.ss_new"))) {
+        file.remove(file.path(dir,"data.ss_new"))
       }
-
-    if (file.exists(ss_new_path)) {
-      file.remove(ss_new_path)
+    ss_new_path <- list.files(dir, pattern = "data.ss_new|data_echo.ss_new", full.names = TRUE)
+    if (length(ss_new_path) > 0) {
+      if (file.exists(ss_new_path)) {
+            file.remove(ss_new_path)
+          }
     }
   }
-
   if (verbose) message("Running SS3.")
   if (os == "unix") {
     system(
@@ -86,7 +83,7 @@ run_ss_model <- function(dir,
     )
   }
   if (check_run == TRUE) {
-    if (!file.exists(ss_new_path)) {
+    if (!file.exists(file.path(dir, "data.ss_new")) && !file.exists(file.path(dir, "data_echo.ss_new"))) {
       if (debug_par_run) {
         test_no_par(
           orig_mod_dir = dir,
@@ -95,12 +92,13 @@ run_ss_model <- function(dir,
         # note that this will exit on error.
       } else {
         stop(
-          "data.ss_new was not created during the model run, which suggests ",
-          "SS3 did not run correctly"
+          "new data file (data.ss_new if using SS3 3.30.18 or data_echo.ss_new",
+          "if using SS3 3.30.21) was not created during the model run, which",
+          "suggests SS3 did not run correctly"
         )
       }
     } else {
-      if (verbose) "data.ss_new created during model run."
+      if (verbose) "new data file (data.ss_new if using SS3 3.30.18 or data_echo.ss_new if using SS3 3.30.21) created during model run."
     }
   }
   Sys.sleep(admb_pause)

R/runSSMSE.R

@@ -95,7 +95,6 @@ run_SSMSE <- function(scen_name_vec,
   if (!is.null(custom_MS_source)) {
     source(custom_MS_source)
   }
-
   # input checks
   if (!all(MS_vec %in% c("EM", "no_catch", "Interim"))) {
     invalid_MS <- MS_vec[unlist(lapply(MS_vec, function(x) !exists(x)))]
@@ -538,7 +537,7 @@ run_SSMSE_iter <- function(out_dir = NULL,
   }
 
   message("Starting iteration ", niter, ".")
-
+  # browser()
   set.seed((iter_seed[["iter"]][1] + 123))
   # get and create directories, copy model files ----
   # assign or reassign OM_dir and OM_in_dir in case they weren't specified
@@ -584,7 +583,6 @@ run_SSMSE_iter <- function(out_dir = NULL,
     sample_struct <- convert_to_r4ss_names(sample_struct)
     sample_struct_hist <- convert_to_r4ss_names(sample_struct_hist)
   }
-
   # Convert the user input parameter modifications into vectors of annual additive deviations
   future_om_dat <- convert_future_om_list_to_devs_df(future_om_list = future_om_list, scen_name = scen_name, niter = niter, om_mod_path = OM_out_dir, nyrs = nyrs, global_seed = (iter_seed[["iter"]][1] + 1234))
 

R/utils.R

@@ -597,8 +597,9 @@ copy_model_files <- function(OM_in_dir = NULL,
                              verbose = FALSE) {
   # checks
   if (!is.null(OM_in_dir)) {
+    dat_file <- list.files(OM_in_dir, pattern = "data.ss_new|data_echo.ss_new")
     if (!all(c(
-      "control.ss_new", "data.ss_new", "starter.ss_new",
+      "control.ss_new", dat_file, "starter.ss_new",
       "forecast.ss_new", "ss.par"
     ) %in% list.files(OM_in_dir))) {
       stop(

tests/testthat/test-develop_OMs.R

@@ -17,7 +17,9 @@ test_that("develop_OMs works as expected", {
   )
   expect_true(file.exists(file.path(temp_path, "cod_SR_BH_steep_0.4", "control.ss_new")))
   expect_true(file.exists(file.path(temp_path, "cod_SR_BH_steep_0.8", "control.ss_new")))
-  dat <- r4ss::SS_readdat(file.path(temp_path, "cod_SR_BH_steep_0.4", "data.ss_new"),
+
+  dat_file <- list.files(file.path(temp_path, "cod_SR_BH_steep_0.4"), pattern = "data.ss_new|data_echo.ss_new")
+  dat <- r4ss::SS_readdat(file.path(temp_path, "cod_SR_BH_steep_0.4", dat_file),
     verbose = FALSE
   )
   ctl <- r4ss::SS_readctl(
@@ -58,7 +60,9 @@ test_that("develop_OMs works as expected when renaming the model", {
   )
   expect_true(file.exists(file.path(temp_path_mod_rename, "rename-mod-test_SR_BH_steep_0.4", "control.ss_new")))
   expect_true(file.exists(file.path(temp_path_mod_rename, "rename-mod-test_SR_BH_steep_0.8", "control.ss_new")))
-  dat <- r4ss::SS_readdat(file.path(temp_path_mod_rename, "rename-mod-test_SR_BH_steep_0.4", "data.ss_new"),
+
+  dat_file <- list.files(file.path(temp_path_mod_rename, "rename-mod-test_SR_BH_steep_0.4"), pattern = "data.ss_new|data_echo.ss_new")
+  dat <- r4ss::SS_readdat(file.path(temp_path_mod_rename, "rename-mod-test_SR_BH_steep_0.4", dat_file),
     verbose = FALSE
   )
   ctl <- r4ss::SS_readctl(

tests/testthat/test-future_om.R

@@ -639,7 +639,8 @@ test_that("Tests a model with env link using historical values", {
     om_mod_path = om_path, nyrs = 10
   )
   expect_length(unique(devs_list[["dev_vals"]][["SR_LN(R0)"]]), 1)
-  dat <- r4ss::SS_readdat(file.path(om_path, "data.ss_new"))
+  OM_dat_file <- list.files(om_path, pattern = "data.ss_new|data_echo.ss_new")
+  dat <- r4ss::SS_readdat(file.path(om_path, OM_dat_file))
   dat <- dat[["envdat"]]
   env_vals <- dat[dat[["Yr"]] >= tmp_list[[1]][["input"]][["first_yr_averaging"]] &
     dat[["Yr"]] <= tmp_list[[1]][["input"]][["last_yr_averaging"]], "Value"]

tests/testthat/test-interim.R

@@ -46,14 +46,19 @@ test_that("run_SSMSE runs with interim assessment workflow", {
   ) # Set a fixed integer seed that allows replication
 
   expect_true(result[["base"]][["errored_iterations"]] == "No errored iterations")
-  expect_true(file.exists(file.path(
-    temp_path, "base", "1", "cod_OM",
-    "data.ss_new"
-  )))
-  expect_true(file.exists(file.path(
-    temp_path, "base", "1", "cod_EM_init",
-    "data.ss_new"
-  )))
+
+  cod_OM_files <- list.files(file.path(temp_path,"base","1","cod_OM"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% cod_OM_files))
+  # expect_true(file.exists(file.path(
+  #   temp_path, "base", "1", "cod_OM",
+  #   "data.ss_new"
+  # )))
+  cod_EM_files <- list.files(file.path(temp_path, "base", "1", "cod_EM_init"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% cod_EM_files))
+  # expect_true(file.exists(file.path(
+  #   temp_path, "base", "1", "cod_EM_init",
+  #   "data.ss_new"
+  # )))
   expect_length(result, 1)
   # could add some better tests to make sure this works.
 })