fix, docs: get set_MSE_seeds to work in readme example

R/runSSMSE.R

@@ -150,14 +150,12 @@ run_SSMSE <- function(scen_list = NULL,
   set.seed(seed=NULL)
   #Now set the global, scenario, and iteration seeds that will be used as needed
   seed<-set_MSE_seeds(seed = seed,
-                      scen_name_vec = scen_list$scen_name_vec,
-                      iter_vec = scen_list$iter_vec)
+                      iter_vec = iter_vec)
 
   # Get directory of base OM files for each scenario as they may be different
   rec_stddev<-rep(0,length(scen_list$scen_name_vec))
   n_impl_error_groups <- rep(0,length(scen_list$scen_name_vec))
   rec_autoCorr<-list()
-
   for(i in 1:length(scen_list$scen_name_vec)){
     if(!is.null(scen_list$OM_in_dir_vec)){
       OM_dir <- locate_in_dirs(scen_list$OM_name_vec[i], scen_list$OM_in_dir_vec[i])

R/utils.R

@@ -741,8 +741,7 @@ copy_SS_inputs <- function(dir.old = NULL,
 #' @param iter_vec The number of iterations per scenario. A vector of integers
 #'  in the same order as scen_name_vec.
 #' @returns A list of length 3 with 1) the global seed value; 2) the scenario seed values; and 3) the iteration seed values.
-#' @example set_MSE_seeds(seed = seq(10, 80, by = 10),
-#'                        iter_vec = c(2, 3))
+#' @example set_MSE_seeds(seed = seq(10, 80, by = 10), iter_vec = c(2, 3))
 set_MSE_seeds<-function(seed = NULL, iter_vec)
 {
   if(is.null(seed)){

README.Rmd

@@ -135,7 +135,7 @@ dir.create(run_res_path)
 # run 1 iteration and 1 scenario of SSMSE using an EM.
 run_SSMSE(scen_name_vec = c("H-ctl", "H-1"), # name of the scenario
           out_dir_scen_vec = run_res_path, # directory in which to run the scenario
-          iter_list = list(1:5, 1:5), # run with 5 iterations each
+          iter_vec = c(5,5), # run with 5 iterations each
           OM_name_vec = NULL, # specify directories instead
           OM_in_dir_vec = c(cod_mod_path, normalizePath(cod_1_path)), # OM files
           EM_name_vec = c("cod", "cod"), # cod is included in package data