Ss3 version 3.30.24.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: SSMSE
 Title: Management Strategy Evaluation (MSE) using Stock Synthesis (SS)
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Kathryn", "Doering", , "kathryn.doering@noaa.gov", role = c("aut", "cre")),
     person("Nathan", "Vaughan", , "nathan.vaughan@noaa.gov", role = "aut")
@@ -43,4 +43,4 @@ Remotes:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -18,7 +18,6 @@ export(plot_comp_sampling)
 export(plot_index_sampling)
 export(run_EM)
 export(run_SSMSE)
-export(run_ss_model)
 export(set_MSE_seeds)
 import(ggplot2)
 import(r4ss)
@@ -32,7 +31,6 @@ importFrom(r4ss,SS_writedat)
 importFrom(r4ss,SS_writeforecast)
 importFrom(r4ss,SS_writestarter)
 importFrom(ss3sim,get_results_all)
-importFrom(ss3sim,get_results_iter)
 importFrom(ss3sim,get_results_scenario)
 importFrom(stats,na.omit)
 importFrom(tidyr,gather)

NEWS.md

@@ -1,5 +1,9 @@
 # SSMSE
 
+## SSMSE 0.4.0
+
+- Update for compatibility with newer Stock Synthesis releases (up to 3.30.24.2), including current file naming conventions such as `ss3.par`, `data_expval.ss`, and `data_boot_001.ss`.
+
 # SSMSE 0.3.0
 
 ## Major changes

R/MS_functions.R

@@ -141,7 +141,7 @@ EM <- function(EM_out_dir = NULL, init_loop = TRUE, OM_dat, verbose = FALSE,
 #' @return A data frame of future catch
 get_EM_catch_df <- function(EM_dir, dat) {
   rpt <- readLines(file.path(EM_dir, "Report.sso"))
-  start <- grep("TIME_SERIES", rpt)
+  start <- grep("^TIME_SERIES", rpt) # need to not match ANNUAL_TIME_SERIES
   start <- start[length(start)] + 1
   end <- grep("SPR_series", rpt, ignore.case = TRUE)
   end <- end[length(end)] - 1
@@ -408,14 +408,15 @@ get_no_EM_catch_df <- function(OM_dir, yrs, MS = "last_yr_catch") {
     verbose = FALSE, readAll = TRUE
   )
   # read par file (using read lines for simplicity.)
-  par <- readLines(file.path(OM_dir, "ss.par"))
+  par_file <- get_ss_par_file(OM_dir)
+  par <- readLines(par_file)
   # use forecasting to find the values desired
   # keep old forecasting
   file.copy(file.path(OM_dir, "forecast.ss"),
     file.path(OM_dir, "forecast_OM.ss"),
     overwrite = TRUE
   )
-  file.copy(file.path(OM_dir, "ss.par"), file.path(OM_dir, "ss_OM.par"),
+  file.copy(par_file, file.path(OM_dir, "ss_OM.par"),
     overwrite = TRUE
   )
   # get the catch values by MS.
@@ -483,14 +484,19 @@ get_no_EM_catch_df <- function(OM_dir, yrs, MS = "last_yr_catch") {
     # TODO: figure out what values should go here; probably not 0.
     Fcast_rec_line <- grep("^# Fcast_recruitments:$", par) + 1
     par[Fcast_rec_line] <- paste0(rep(0, fore[["Nforecastyrs"]]), collapse = " ")
-    Fcast_impl_err_line <- grep("^# Fcast_impl_error:$", par) + 1
-    par[Fcast_impl_err_line] <- paste0(rep(0, fore[["Nforecastyrs"]]), collapse = " ")
-    writeLines(par, file.path(OM_dir, "ss.par"))
+    # # Forecast implementation error parameters were included in earlier SS3 version 
+    # # whether specified by the user or not. These changes are not needed in 3.30.24.
+    # Fcast_impl_err_line <- grep("^# Fcast_impl_error:$", par) + 1
+    # par[Fcast_impl_err_line] <- paste0(rep(0, fore[["Nforecastyrs"]]), collapse = " ")
+    writeLines(par, par_file)
     # Run SS3 with the new catch set as forecast targets. This will use SS3 to
     # calculate the F required in the OM to achieve these catches.
-    run_ss_model(OM_dir, "-maxfn 0 -phase 50 -nohess",
-      verbose = FALSE,
-      debug_par_run = TRUE
+    r4ss::run(
+      dir = OM_dir,
+      exe = get_bin(),
+      extras = "-maxfn 0 -phase 50 -nohess",
+      skipfinished = FALSE,
+      verbose = FALSE
     )
     # Load the SS3 results
     outlist <- r4ss::SS_output(OM_dir,
@@ -529,7 +535,7 @@ get_no_EM_catch_df <- function(OM_dir, yrs, MS = "last_yr_catch") {
     file.path(OM_dir, "forecast.ss"),
     overwrite = TRUE
   )
-  file.copy(file.path(OM_dir, "ss_OM.par"), file.path(OM_dir, "ss.par"),
+  file.copy(file.path(OM_dir, "ss_OM.par"), par_file,
     overwrite = TRUE
   )
   return_list <- list(
@@ -593,7 +599,12 @@ Interim <- function(EM_out_dir = NULL, EM_init_dir = NULL,
     )
     Reference_ctl <- SS_readctl(file = file.path(EM_out_dir, start[["ctlfile"]]), use_datlist = TRUE, datlist = Reference_dat, verbose = FALSE)
     Reference_forecast <- SS_readforecast(file.path(EM_out_dir, "forecast.ss"), verbose = FALSE)
-    Reference_par <- SS_readpar_3.30(parfile = file.path(EM_out_dir, "ss.par"), datsource = Reference_dat, ctlsource = Reference_ctl, verbose = FALSE)
+    Reference_par <- SS_readpar_3.30(
+      parfile = get_ss_par_file(EM_out_dir),
+      datsource = Reference_dat,
+      ctlsource = Reference_ctl,
+      verbose = FALSE
+    )
     SS_writestarter(
       mylist = start,
       dir = EM_out_dir,
@@ -611,12 +622,18 @@ Interim <- function(EM_out_dir = NULL, EM_init_dir = NULL,
     temp_forecast[, 1] <- (Reference_dat[["endyr"]] + 1 - forecast_adjust):(Reference_dat[["endyr"]] + Reference_forecast[["Nforecastyrs"]])
     colnames(temp_forecast) <- c("year", "recdev")
     Reference_par[["recdev_forecast"]] <- as.data.frame(temp_forecast)
-    temp_impl_error <- matrix(0, nrow = (Reference_forecast[["Nforecastyrs"]]), ncol = 2)
-    temp_impl_error[, 1] <- (Reference_dat[["endyr"]] + 1):(Reference_dat[["endyr"]] + Reference_forecast[["Nforecastyrs"]])
-    colnames(temp_impl_error) <- c("year", "impl_error")
-    Reference_par[["Fcast_impl_error"]] <- as.data.frame(temp_impl_error)
-
-    SS_writepar_3.30(parlist = Reference_par, outfile = file.path(EM_out_dir, "ss.par"), overwrite = TRUE)
+    # # Forecast implementation error parameters were included in earlier SS3 version 
+    # # whether specified by the user or not. These changes are not needed in 3.30.24.
+    # temp_impl_error <- matrix(0, nrow = (Reference_forecast[["Nforecastyrs"]]), ncol = 2)
+    # temp_impl_error[, 1] <- (Reference_dat[["endyr"]] + 1):(Reference_dat[["endyr"]] + Reference_forecast[["Nforecastyrs"]])
+    # colnames(temp_impl_error) <- c("year", "impl_error")
+    # Reference_par[["Fcast_impl_error"]] <- as.data.frame(temp_impl_error)
+
+    SS_writepar_3.30(
+      parlist = Reference_par,
+      outfile = get_ss_par_file(EM_out_dir),
+      overwrite = TRUE
+    )
 
     SS_writeforecast(
       mylist = Reference_forecast,
@@ -674,15 +691,20 @@ Interim <- function(EM_out_dir = NULL, EM_init_dir = NULL,
     run_EM(EM_dir = EM_out_dir, verbose = verbose, check_converged = TRUE)
 
 
-    data_filename <- list.files(file.path(EM_out_dir), pattern = "data.ss_new|data_expval.ss")
-    if (data_filename == "data.ss_new") {
-      exp_vals <- SS_readdat(file.path(EM_out_dir, data_filename),
-        section = 2, # expected values data file in v3.30.21
+    exp_filename <- get_data_file(EM_out_dir, "expected")
+    if (is.null(exp_filename)) {
+      stop(
+        "Could not find an expected-values data file in ", EM_out_dir,
+        ". Expected data_expval.ss or an older data.ss_new style output."
+      )
+    }
+    if (exp_filename %in% c("data.ss_new", "data_echo.ss_new")) {
+      exp_vals <- SS_readdat(file.path(EM_out_dir, exp_filename),
+        section = 2,
         verbose = FALSE
       )
     } else {
-      # for SS3 v3.30.21
-      exp_vals <- r4ss::SS_readdat(file.path(EM_out_dir, "data_expval.ss"),
+      exp_vals <- r4ss::SS_readdat(file.path(EM_out_dir, exp_filename),
         verbose = FALSE
       )
     }

R/calc_F.R

@@ -11,7 +11,7 @@
 #' @importFrom tidyr gather separate
 #' @return a list containing: F_df, a long dataframe with F by year, Era, Seas,
 #'  and fleet; F_rate, a data frame with F for the time frame of the model
-#'  only by year, Seas, and fleet, ordered as the ss.par file expects; init_F,
+#'  only by year, Seas, and fleet, ordered as the ss3.par file expects; init_F,
 #'  a named vector of initial F values by Season and fleet, ordered (and named)
 #'  as SS expects; and F_rate_fcast, a dataframe of forecasted F by year, Seas,
 #'  and fleet, ordered as SS would expect in F_rate.

R/develop_OMs.R

@@ -13,11 +13,22 @@
 #' @param hess Should the hessian be estimated if reffiting the OMs? defaults to
 #'  FALSE
 #' @export
-develop_OMs <- function(OM_name = NULL, OM_in_dir = NULL, out_dir = getwd(), par_name, par_vals,
-                        refit_OMs = TRUE, hess = FALSE) {
+develop_OMs <- function(
+  OM_name = NULL,
+  OM_in_dir = NULL,
+  out_dir = getwd(),
+  par_name,
+  par_vals,
+  refit_OMs = TRUE,
+  hess = FALSE
+) {
   # check input
-  if (!is.null(OM_name)) assertive.types::assert_is_a_string(OM_name)
-  if (!is.null(OM_in_dir)) assertive.types::assert_is_a_string(OM_in_dir)
+  if (!is.null(OM_name)) {
+    assertive.types::assert_is_a_string(OM_name)
+  }
+  if (!is.null(OM_in_dir)) {
+    assertive.types::assert_is_a_string(OM_in_dir)
+  }
   assertive.types::assert_is_a_string(out_dir)
   assertive.types::assert_is_a_string(par_name)
   assertive.properties::assert_is_atomic(par_vals)
@@ -40,11 +51,16 @@ develop_OMs <- function(OM_name = NULL, OM_in_dir = NULL, out_dir = getwd(), par
     OM_in_dir <- pkg_dirs[grep(OM_name, pkg_dirs)]
     if (length(OM_in_dir) != 1) {
       stop(
-        "OM_name ", OM_name, " matched ", length(OM_in_dir), " models in ",
+        "OM_name ",
+        OM_name,
+        " matched ",
+        length(OM_in_dir),
+        " models in ",
         "SSMSE external package data, but should match 1. Please ",
         "change OM_name to match (or partially match unambiguously) with 1 ",
         "model in the models folder of the SSMSE external package data. ",
-        "Model options are: ", paste0(basename(pkg_dirs), collapse = ", ")
+        "Model options are: ",
+        paste0(basename(pkg_dirs), collapse = ", ")
       )
     }
   }
@@ -58,7 +74,7 @@ develop_OMs <- function(OM_name = NULL, OM_in_dir = NULL, out_dir = getwd(), par
     #         " If parameter devs are desired, use refit_OMs = TRUE.")
     # read in parfile to save the recdevs.
     parfile <- r4ss::SS_readpar_3.30(
-      parfile = file.path(OM_in_dir, "ss.par"),
+      parfile = get_ss_par_file(OM_in_dir),
       datsource = file.path(OM_in_dir, start[["datfile"]]),
       ctlsource = file.path(OM_in_dir, start[["ctlfile"]]),
       verbose = FALSE
@@ -83,64 +99,91 @@ develop_OMs <- function(OM_name = NULL, OM_in_dir = NULL, out_dir = getwd(), par
       to = tmp_mod_path
     )
     r4ss::SS_changepars(
-      dir = tmp_mod_path, ctlfile = "control.ss_new",
-      newctlfile = "control_modified.ss", strings = par_name,
-      newvals = i, verbose = FALSE
+      dir = tmp_mod_path,
+      ctlfile = "control.ss_new",
+      newctlfile = "control_modified.ss",
+      strings = par_name,
+      newvals = i,
+      verbose = FALSE
     )
     # remove files with old values
     file.remove(file.path(tmp_mod_path, "control.ss_new"))
     file.remove(file.path(tmp_mod_path, start[["ctlfile"]]))
-    file.remove(file.path(tmp_mod_path, "ss.par"))
+    par_file <- get_ss_par_file(tmp_mod_path)
+    if (file.exists(par_file)) {
+      file.remove(par_file)
+    }
+    # also delete older name of .par file if they exist
+    if (file.exists(file.path(tmp_mod_path, "ss.par"))) {
+      file.remove(file.path(tmp_mod_path, "ss.par"))
+    }
     file.rename(
       from = file.path(tmp_mod_path, "control_modified.ss"),
       to = file.path(tmp_mod_path, start[["ctlfile"]])
     )
     if (refit_OMs == TRUE) {
-      run_ss_model(
+      r4ss::run(
         dir = tmp_mod_path,
-        admb_options = opts,
+        exe = get_bin(),
+        extras = opts,
+        skipfinished = FALSE,
         verbose = FALSE
       )
       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"))) {
+      if (
+        # if redundant files exist, delete the one with the old name
+        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(
+      r4ss::run(
         dir = tmp_mod_path,
-        admb_options = "-maxfn 0 -phase 50 -nohess",
+        exe = get_bin(),
+        extras = "-maxfn 0 -phase 50 -nohess",
+        skipfinished = FALSE,
         verbose = FALSE
       )
       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"))) {
+      if (
+        # if redundant files exist, delete the one with the old name
+        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"),
+        parfile = get_ss_par_file(tmp_mod_path),
         datsource = file.path(tmp_mod_path, start[["datfile"]]),
-        ctlsource = file.path(tmp_mod_path, start[["ctlfile"]]), verbose = FALSE
+        ctlsource = file.path(tmp_mod_path, start[["ctlfile"]]),
+        verbose = FALSE
       )
       if (!is.null(new_parfile[["recdev1"]])) {
         recdev_name <- "recdev1"
       } else {
         recdev_name <- "recdev2"
       }
-      new_parfile[[recdev_name]][, "recdev"] <- parfile[[recdev_name]][, "recdev"]
+      new_parfile[[recdev_name]][, "recdev"] <- parfile[[recdev_name]][,
+        "recdev"
+      ]
 
       # add back original F estimates for F method 2 assessments otherwise they all default to 0.05
       if (!is.null(new_parfile[["F_rate"]])) {
         new_parfile[["F_rate"]][, "F"] <- parfile[["F_rate"]][, "F"]
       }
 
-      r4ss::SS_writepar_3.30(new_parfile,
-        outfile = file.path(tmp_mod_path, "ss.par"),
-        verbose = FALSE, overwrite = TRUE
+      r4ss::SS_writepar_3.30(
+        new_parfile,
+        outfile = get_ss_par_file(tmp_mod_path),
+        verbose = FALSE,
+        overwrite = TRUE
       )
     }
   }