Update: added fixed seed

Added seed input to example and adjusted the revdev and impl error inputs to be single values. The code is not set up to accept scenario specific strategies yet.

README.Rmd

@@ -143,9 +143,10 @@ run_SSMSE(scen_name_vec = c("H-ctl", "H-1"), # name of the scenario
           use_SS_boot_vec = c(TRUE, TRUE), # use the SS bootstrap module for sampling
           nyrs_vec = c(6, 6),        # Years to project OM forward
           nyrs_assess_vec = c(3, 3), # Years between assessments
-          rec_dev_pattern = c("none", "none"), # Don't use recruitment deviations
-          impl_error_pattern = c("none", "none"), # Don't use implementation error
-          sample_struct_list = sample_struct_list) # How to sample data for running the EM.
+          rec_dev_pattern = c("none"), # Don't use recruitment deviations
+          impl_error_pattern = c("none"), # Don't use implementation error
+          sample_struct_list = sample_struct_list, # How to sample data for running the EM.
+          seed = 12345) #Set a fixed integer seed that allows replication 
 ```
 
 The function `SSMSE_summary_all` can be used to summarize the model results in a list of dataframes. Note that if you have issues, try reinstalling SSMSE using `remotes::install_github("nmfs-fish-tools/SSMSE")` and restarting your R session. Also, make sure you are using the development branch versions of [r4ss](https://github.com/r4ss/r4ss) and [ss3sim](https://github.com/ss3sim/ss3sim) (by installing `remotes::install_github("r4ss/r4ss@development")` and `remotes::install_github("ss3sim/ss3sim@development")`. These versions should be installed automatically when SSMSE is downloaded.

README.md

@@ -93,6 +93,7 @@ library(r4ss) #install using remotes::install_github("r4ss/r4ss@development)
 # Create a folder for the output in the working directory.
 run_SSMSE_dir <- file.path("run_SSMSE-ex")
 dir.create(run_SSMSE_dir)
+## Warning in dir.create(run_SSMSE_dir): 'run_SSMSE-ex' already exists
 ```
 
 The cod model with H = 0.65 is included as external package data.
@@ -105,7 +106,10 @@ cod_mod_path <- system.file("extdata", "models", "cod", package = "SSMSE")
 file.copy(from = cod_mod_path, to = run_SSMSE_dir, recursive = TRUE)
 ## [1] TRUE
 file.rename(from = file.path(run_SSMSE_dir, "cod"), to = file.path(run_SSMSE_dir, "cod-1"))
-## [1] TRUE
+## Warning in file.rename(from = file.path(run_SSMSE_dir, "cod"), to =
+## file.path(run_SSMSE_dir, : cannot rename file 'run_SSMSE-ex/cod' to 'run_SSMSE-
+## ex/cod-1', reason 'Access is denied'
+## [1] FALSE
 cod_1_path <- file.path(run_SSMSE_dir, "cod-1")
 # make model read initial values from control file and not ss.par
 start <- r4ss::SS_readstarter(file = file.path(cod_1_path, "starter.ss"), verbose = FALSE)
@@ -118,14 +122,14 @@ r4ss::SS_changepars(dir = cod_1_path, ctlfile = "control.ss_new",
 ## [1] "SR_BH_steep"
 ## These are the ctl file lines as they currently exist:
 ##      LO HI INIT PRIOR PR_SD PR_type PHASE env_var&link dev_link dev_minyr
-## 107 0.2  1 0.65   0.7  0.05       0    -4            0        0         0
+## 107 0.2  1    1   0.7  0.05       0    -4            0        0         0
 ##     dev_maxyr dev_PH Block Block_Fxn       Label Linenum
 ## 107         0      0     0         0 SR_BH_steep     107
 ## line numbers in control file (n=1):
 ## 107
 ## wrote new file to control_modified.ss with the following changes:
 ##   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior
-## 1    0.65       1       -4       -4    0.2    0.2      1      1      0.7
+## 1       1       1       -4       -4    0.2    0.2      1      1      0.7
 ##   newprior oldprsd newprsd oldprtype newprtype       comment
 ## 1      0.7    0.05    0.05         0         0 # SR_BH_steep
 # remove files with M = 0.2
@@ -221,9 +225,10 @@ run_SSMSE(scen_name_vec = c("H-ctl", "H-1"), # name of the scenario
           use_SS_boot_vec = c(TRUE, TRUE), # use the SS bootstrap module for sampling
           nyrs_vec = c(6, 6),        # Years to project OM forward
           nyrs_assess_vec = c(3, 3), # Years between assessments
-          rec_dev_pattern = c("none", "none"), # Don't use recruitment deviations
-          impl_error_pattern = c("none", "none"), # Don't use implementation error
-          sample_struct_list = sample_struct_list) # How to sample data for running the EM.
+          rec_dev_pattern = c("none"), # Don't use recruitment deviations
+          impl_error_pattern = c("none"), # Don't use implementation error
+          sample_struct_list = sample_struct_list, # How to sample data for running the EM.
+          seed = 12345) #Set a fixed integer seed that allows replication 
 ```
 
 The function `SSMSE_summary_all` can be used to summarize the model
@@ -241,8 +246,12 @@ should be installed automatically when SSMSE is downloaded.
 # Summarize 1 iteration of output
 summary <- SSMSE_summary_all(normalizePath(run_res_path))
 ## Extracting results from 2 scenarios
-## Starting H-1 with 5 iterations
-## Starting H-ctl with 5 iterations
+## Warning in ss3sim::get_results_all(directory = dir, user_scenarios = scenarios):
+## ss3sim_scalar.csv already exists and overwrite_files = FALSE, so a new file was
+## not written
+## Warning in ss3sim::get_results_all(directory = dir, user_scenarios = scenarios):
+## ss3sim_ts.csv already exists and overwrite_files = FALSE, so a new file was not
+## written
 ```
 
 Plotting and data manipulation can then be done with these summaries.
@@ -254,6 +263,7 @@ in year 103 (cod\_EM\_103), and the EM run with last year of data in 106
 
 ``` r
 library(ggplot2) # use install.packages("ggplot2") to install package if needed
+## Warning: package 'ggplot2' was built under R version 4.0.2
 library(tidyr) # use install.packages("tidyr") to install package if needed
 ## 
 ## Attaching package: 'tidyr'