fix: small changes to get ssmse to run with a custom managment strategy

This checks that the routine can run all the way through, but not that it is doing what it should be, so more debugging may be necessary
nmfs-fish-tools · Oct 21, 2020 · 7a41e1c · 7a41e1c
1 parent feb83da
commit 7a41e1c
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Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/R/parse_MS.R b/R/parse_MS.R
@@ -519,8 +519,6 @@ parse_MS <- function(MS, EM_out_dir = NULL, EM_init_dir = NULL,
                       yrs = (OM_dat$endyr + 1):(OM_dat$endyr + nyrs_assess),
                       MS = MS)
   } else {
-    warning("MS = custom is still in development. Please report bugs to ",
-            "github.com/nmfs-fish-tools/SSMSE/issues")
     pars_list <- list(EM_out_dir = EM_out_dir,
                       EM_init_dir = EM_init_dir, 
                       init_loop = init_loop, 

diff --git a/R/runSSMSE.R b/R/runSSMSE.R
@@ -178,7 +178,7 @@ run_SSMSE <- function(scen_name_vec,
   impl_error_pattern <- match.arg(impl_error_pattern, 
                                   choices = c("none", "rand", "user"))
   if(!all(MS_vec %in% c("EM", "no_catch", "Interim"))) {
-    invalid_MS <- MS_vec[unlist(lapply(MS_vec, !exists))]
+    invalid_MS <- MS_vec[unlist(lapply(MS_vec, function(x) !exists(x)))]
     invalid_MS <- invalid_MS[!invalid_MS %in% c("EM", "no_catch", "Interim")]
     if(length(invalid_MS) > 0) {
       stop("Invalid management strategies in MS_vec: ",
@@ -687,6 +687,8 @@ run_SSMSE_iter <- function(out_dir = NULL,
   EM_out_dir <- out_loc[["EM_out_dir"]]
   if (!is.null(EM_out_dir)) {
     EM_out_dir_basename <- strsplit(EM_out_dir, "_init$")[[1]][1]
+  } else {
+    EM_out_dir_basename <- NULL
   }
   copy_model_files(OM_in_dir = OM_in_dir, OM_out_dir = OM_out_dir,
                    EM_in_dir = EM_in_dir, EM_out_dir = EM_out_dir)
@@ -738,7 +740,7 @@ run_SSMSE_iter <- function(out_dir = NULL,
   new_catch_list <- parse_MS(MS = MS, EM_out_dir = EM_out_dir, init_loop = TRUE,
                            OM_dat = OM_dat, OM_out_dir = OM_out_dir,
                            verbose = verbose, nyrs_assess = nyrs_assess,
-                           interim_struct = interim_struct,
+                           interim_struct = interim_struct, dat_yrs = NA,
                            seed = (iter_seed$iter[1]+123456))
 
   message("Finished getting catch (years ",
@@ -825,9 +827,14 @@ run_SSMSE_iter <- function(out_dir = NULL,
       # Only want data for the new years: (yr+nyrs_assess):yr
       # create the new dataset to input into the EM
       # loop EM and get management quantities.
+      if(!is.null(EM_out_dir_basename)) {
+        tmp_EM_init_dir <- paste0(EM_out_dir_basename, "_init")
+      } else {
+        tmp_EM_init_dir <- NULL
+      }
       new_catch_list <- parse_MS(MS = MS,
                                  EM_out_dir = EM_out_dir,
-                                 EM_init_dir = paste0(EM_out_dir_basename, "_init"),
+                                 EM_init_dir = tmp_EM_init_dir,
                                  OM_dat = new_OM_dat,
                                  init_loop = FALSE, verbose = verbose,
                                  nyrs_assess = nyrs_assess,