fix more warnings

nmfs-fish-tools · Jun 5, 2024 · 2f84d16 · 2f84d16
1 parent 2942c60
commit 2f84d16
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Showing 7 changed files with 130 additions and 86 deletions.
diff --git a/R/develtools.R b/R/develtools.R
@@ -29,34 +29,36 @@ test_no_par <- function(orig_mod_dir, new_mod_dir) {
   # read in the 2 par files.
   orig_par <- readLines(file.path(orig_mod_dir, "ss.par"))
 
-  dat_file <- list.files(file.path(new_mod_dir), pattern = "data.ss_new|data_echo.ss_new")
+  dat_file <- list.files(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)
-      orig_par_names <- grep("^# [^N]", orig_par, value = TRUE)
-      missing_vars <- setdiff(new_par_names, orig_par_names)
-      if (length(orig_par) < length(new_par)) {
-        msg <- " is missing the "
+  if (length(dat_file) > 0) {
+    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)
+        orig_par_names <- grep("^# [^N]", orig_par, value = TRUE)
+        missing_vars <- setdiff(new_par_names, orig_par_names)
+        if (length(orig_par) < length(new_par)) {
+          msg <- " is missing the "
+        }
+        if (length(orig_par) > length(new_par)) {
+          msg <- " has added "
+        }
+        stop(
+          "Problem with the ss.par file - different number of lines. ",
+          "The original par file in ", orig_mod_dir, msg, " parameters: ",
+          paste0(missing_vars, collapse = ", ")
+        )
+      } else {
+        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 ",
+          "par in ", new_mod_dir, ", so not sure what the issue is."
+        )
       }
-      if (length(orig_par) > length(new_par)) {
-        msg <- " has added "
-      }
-      stop(
-        "Problem with the ss.par file - different number of lines. ",
-        "The original par file in ", orig_mod_dir, msg, " parameters: ",
-        paste0(missing_vars, collapse = ", ")
-      )
-    } else {
-      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 ",
-        "par in ", new_mod_dir, ", so not sure what the issue is."
-      )
+      # TODO: develop some more sophisticated ways to look at par file diffs.
     }
-    # TODO: develop some more sophisticated ways to look at par file diffs.
   } else {
     # problem is not with the par file, but with some other model misspecification.
     stop(

diff --git a/R/initOM.R b/R/initOM.R
@@ -492,17 +492,30 @@ run_OM <- function(OM_dir,
         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
-  )
+  if(data_filename == "data.ss_new"){
+    dat <- r4ss::SS_readdat(file.path(OM_dir, data_filename),
+      section = max_section, #bootstrap file in v3.30.21
+      verbose = FALSE
+    )
+  } else {
+    # for SS3 v3.30.21
+    dat <- r4ss::SS_readdat(file.path(OM_dir, "data_boot_001.ss"),
+      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_filename),
-      section = 2,
-      verbose = FALSE
-    )
+    if(data_filename == "data.ss_new"){
+      exp_vals <- r4ss::SS_readdat(file.path(OM_dir, data_filename),
+        section = 2, #expected values data file in v3.30.21
+        verbose = FALSE
+      )
+    } else {
+      # for SS3 v3.30.21
+      exp_vals <- r4ss::SS_readdat(file.path(OM_dir, "data_expval.ss"),
+        verbose = FALSE
+      )
+    }
     dat[["catch"]] <- exp_vals[["catch"]]
   }
   return(dat)

diff --git a/R/results.R b/R/results.R
@@ -141,25 +141,45 @@ plot_index_sampling <- function(dir = getwd()) {
   assertive.types::assert_is_a_string(om_name)
 
   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]),
-      om_name, data_file
-    ),
-    verbose = FALSE, section = 1
-  )
+  if (data_file == "data.ss_new") {
+    tmp_dat_OM <- r4ss::SS_readdat(
+      file.path(
+        dir, as.character(iters[1]),
+        om_name, data_file
+      ),
+      verbose = FALSE, section = 1
+    )
+  } else {
+    tmp_dat_OM <- r4ss::SS_readdat(
+      file.path(
+        dir, as.character(iters[1]),
+        om_name, data_file
+      ),
+      verbose = FALSE
+    ) 
+  }
   tmp_dat_OM[["CPUE"]][["iteration"]] <- as.character(iters[1])
   tmp_dat_OM[["CPUE"]][["scenario"]] <- scenario
   tmp_dat_OM[["CPUE"]][["model_run"]] <- "historical_values"
   index_dat <- tmp_dat_OM[["CPUE"]]
   # get the OM expected values
-  tmp_dat_OM <- r4ss::SS_readdat(
-    file.path(
-      dir, as.character(iters[1]),
-      om_name, data_file
-    ),
+  if (data_file == "data.ss_new") {
+    tmp_dat_OM <- r4ss::SS_readdat(
+      file.path(
+        dir, as.character(iters[1]),
+        om_name, data_file
+      ),
     verbose = FALSE, section = 2
-  )
+    )
+  } else {
+    tmp_dat_OM <- r4ss::SS_readdat(
+      file.path(
+        dir, as.character(iters[1]),
+        om_name, "data_expval.ss"
+      ),
+      verbose = FALSE
+    )
+  }
   tmp_dat_OM[["CPUE"]][["iteration"]] <- as.character(iters[1])
   tmp_dat_OM[["CPUE"]][["scenario"]] <- scenario
   tmp_dat_OM[["CPUE"]][["model_run"]] <- "OM_expected_values"
@@ -172,13 +192,24 @@ plot_index_sampling <- function(dir = getwd()) {
   ), value = TRUE)
   assertive.types::assert_is_a_string(em_name)
   for (i in iters) {
-    tmp_dat_EM <- r4ss::SS_readdat(
-      file.path(
-        dir, as.character(i),
-        em_name, "data.ss_new"
-      ),
-      verbose = FALSE, section = 1
-    )
+    if(data_file == "data.ss_new"){
+      tmp_dat_EM <- r4ss::SS_readdat(
+        file.path(
+          dir, as.character(i),
+          em_name, data_file
+        ),
+        verbose = FALSE, section = 1
+      )
+    } else {
+      tmp_dat_EM <- r4ss::SS_readdat(
+        file.path(
+          dir, as.character(i),
+          em_name, data_file
+        ),
+        verbose = FALSE
+      )
+    }
+
     tmp_dat_EM[["CPUE"]][["iteration"]] <- i
     tmp_dat_EM[["CPUE"]][["scenario"]] <- scenario
     tmp_dat_EM[["CPUE"]][["model_run"]] <- "sampled_dataset"
@@ -364,10 +395,16 @@ get_performance_metrics <- function(dir = getwd(),
           )
         }
         om_mod_path <- tmp_mods[om_mod]
-        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
+        om_mod_dat <- list.files(om_mod_path, pattern = "data.ss_new|data_echo.ss_new")
+        if(om_mod_dat == "data.ss_new"){
+          dat <- r4ss::SS_readdat(file.path(om_mod_path, om_mod_dat),
+            section = 1, verbose = FALSE
         )
+        } else {
+          dat <- r4ss::SS_readdat(file.path(om_mod_path, om_mod_dat),
+           verbose = FALSE
+        )
+        }
         tmp_catch <- dat[["catch"]]
         tmp_catch <- tmp_catch[, c("year", "fleet", "catch")]
         colnames(tmp_catch) <- c("year", "fleet", "value")

diff --git a/R/runSS.R b/R/runSS.R
@@ -92,9 +92,9 @@ run_ss_model <- function(dir,
         # note that this will exit on error.
       } else {
         stop(
-          "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"
+          "New data file (data.ss_new if using SS3 v3.30.18 or data_echo.ss_new ",
+          "if using SS3 v3.30.21) was not created during the model run, which ",
+          "suggests SS3 did not run correctly."
         )
       }
     } else {

diff --git a/R/runSSMSE.R b/R/runSSMSE.R
@@ -305,7 +305,6 @@ run_SSMSE_scen <- function(scen_name = "scen_1",
   if (!is.null(sample_struct_hist)) assertive.types::assert_is_list(sample_struct_hist)
   assertive.types::assert_is_a_bool(verbose)
 
-
   # create the out_dir to store all files for all iter in the scenario.
   if (is.null(out_dir_scen)) {
     out_dir_iter <- scen_name
@@ -537,7 +536,6 @@ 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

diff --git a/tests/testthat/test-runSSMSE.R b/tests/testthat/test-runSSMSE.R
@@ -23,7 +23,6 @@ test_that("run_SSMSE_iter runs with no EM", {
 
   cod_OM_files <- list.files(file.path(new_temp_path, "1", "cod_OM"))
   expect_true(any(c("data.ss_new","data_echo.ss_new") %in% cod_OM_files))
-  # expect_true(file.exists(file.path(new_temp_path, "1", "cod_OM", "data.ss_new")))
   expect_true(result)
 })
 
@@ -54,13 +53,11 @@ test_that("run_SSMSE runs with an EM, and works with summary funs", {
   )) # Set a fixed integer seed that allows replication
   expect_equivalent(result[["H-ctl"]][["errored_iterations"]], "No errored iterations")
 
-  H-ctl_cod_OM_files <- list.files(file.path(temp_path, "H-ctl", "1", "cod_OM"))
-  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% H-ctl_cod_OM_files))
-  # expect_true(file.exists(file.path(temp_path, "H-ctl", "1", "cod_OM", "data.ss_new")))
+  Hctl_cod_OM_files <- list.files(file.path(temp_path, "H-ctl", "1", "cod_OM"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% Hctl_cod_OM_files))
 
-  H-ctl_cod_EM_files <- list.files(file.path(temp_path, "H-ctl", "1", "cod_EM_106"))
-  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% H-ctl_cod_EM_files))
-  # expect_true(file.exists(file.path(temp_path, "H-ctl", "1", "cod_EM_106", "data.ss_new")))
+  Hctl_cod_EM_files <- list.files(file.path(temp_path, "H-ctl", "1", "cod_EM_106"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% Hctl_cod_EM_files))
 
   expect_length(result, 1)
   # some more specific values, specific to the scenario above.
@@ -117,10 +114,10 @@ test_that("run_SSMSE runs multiple iterations/scenarios and works with summary f
     seed = 12345
   )) # Set a fixed integer seed that allows replication
   expect_equivalent(result[["H-ctl"]][["errored_iterations"]], "No errored iterations")
-  H-ctl_cod_OM_files <- list.files(file.path(new_temp_path, "H-ctl", "1", "cod_OM"))
-  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% H-ctl_cod_OM_files))
-  H-ctl_cod_EM_103_files <- list.files(file.path(new_temp_path, "H-ctl", "1", "cod_EM_103"))
-  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% H-ctl_cod_EM_103_files))
+  Hctl_cod_OM_files <- list.files(file.path(new_temp_path, "H-ctl", "1", "cod_OM"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% Hctl_cod_OM_files))
+  Hctl_cod_EM_103_files <- list.files(file.path(new_temp_path, "H-ctl", "1", "cod_EM_103"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% Hctl_cod_EM_103_files))
   # this file should not exist b/c run_EM_last_yr is FALSE.
   # expect_true(!file.exists(
   #   file.path(new_temp_path, "H-ctl", "1", "cod_EM_106", "data.ss_new")
@@ -129,15 +126,12 @@ test_that("run_SSMSE runs multiple iterations/scenarios and works with summary f
     result[["H-scen-2"]][["errored_iterations"]],
     "No errored iterations"
   )
-  H-scen2_cod_OM_files <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_OM"))
-  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% H-scen2_cod_OM_files))
-  H-scen2_cod_EM_103_files <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_EM_103"))
-  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% H-scen2_cod_EM_103_files))
-  H-scen2_cod_EM_106_files <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_EM_106"))
-  expect_true(!any(c("data.ss_new","data_echo.ss_new") %in% H-scen2_cod_EM_106_files))
-  # expect_true(!file.exists(
-  #   file.path(new_temp_path, "H-scen-2", "1", "cod_EM_106", "data.ss_new")
-  # ))
+  Hscen2_cod_OM_files <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_OM"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% Hscen2_cod_OM_files))
+  Hscen2_cod_EM_103_files <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_EM_103"))
+  expect_true(any(c("data.ss_new","data_echo.ss_new") %in% Hscen2_cod_EM_103_files))
+  Hscen2_cod_EM_106_files <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_EM_106"))
+  expect_true(!any(c("data.ss_new","data_echo.ss_new") %in% Hscen2_cod_EM_106_files))
   expect_length(result, 2)
   # summarize results
   summary <- SSMSE_summary_all(dir = new_temp_path, run_parallel = FALSE)
@@ -146,7 +140,7 @@ test_that("run_SSMSE runs multiple iterations/scenarios and works with summary f
 
   # calculate performance metrics
   # to use in the tests
-  dat_file <- list.files(file.path(temp_path, "H-scen-2", "1", "cod_OM"), pattern = "data.ss_new|data_echo.ss_new")
+  dat_file <- list.files(file.path(new_temp_path, "H-scen-2", "1", "cod_OM"), pattern = "data.ss_new|data_echo.ss_new")
   tmp_dat <- r4ss::SS_readdat(
     file.path(new_temp_path, "H-scen-2", "1", "cod_OM", dat_file)
   )

diff --git a/tests/testthat/test_develtools.R b/tests/testthat/test_develtools.R
@@ -25,8 +25,8 @@ r4ss::SS_writestarter(start_orig,
 # mock a bad par file by deleting a line
 orig_par <- readLines(file.path(orig_mod_dir, "ss.par"))
 writeLines(orig_par, file.path(temp_path, "good_ss.par"))
-fcast_imp_line <- grep("^# Fcast_impl_error:$", orig_par)
-bad_par <- orig_par[-c(fcast_imp_line, fcast_imp_line + 1)]
+fcast_line <- grep("^# Fcast_impl_error:$|^# Fcast_recruitments:$", orig_par)
+bad_par <- orig_par[-c(fcast_line, fcast_line + 1)]
 writeLines(bad_par, file.path(orig_mod_dir, "ss.par"))
 new_mod_dir <- file.path(temp_path, "new_mod_dir")
 
@@ -36,9 +36,9 @@ test_that("test_no_par works as expected", {
     run_ss_model(orig_mod_dir, "-maxfn 0 -phase 50 -nohess",
       verbose = FALSE
     ),
-    "data.ss_new was not created during the model run",
+    "New data file (data.ss_new if using SS3 v3.30.18 or data_echo.ss_new ",
     fixed = TRUE
-  )
+    )
   expect_error(
     test_no_par(
       orig_mod_dir = orig_mod_dir,