diff --git a/README.Rmd b/README.Rmd index aedd2277..b1ceea54 100644 --- a/README.Rmd +++ b/README.Rmd @@ -82,18 +82,16 @@ Note that this is a simple example and not a true MSE, so the OM and EM structur ### Setup R workspace folders First, we will load the `SSMSE` package and create a folder in which to run the example: -```{r, eval=FALSE} +```{r, echo=FALSE, results="hide"} +devtools::install_local(".", upgrade = "never", quiet = TRUE) +``` +```{r, eval=TRUE} library(SSMSE) #load the package library(r4ss) #install using remotes::install_github("r4ss/r4ss@development) library(foreach) #if using run_parallel = TRUE library(doParallel) #if using run_parallel = TRUE ``` -```{r, echo=FALSE, results="hide"} -devtools::load_all(".") # for rendering this readme when it is in the SSMSE pkg -library(r4ss) -library(foreach) #if using run_parallel = TRUE -library(doParallel) #if using run_parallel = TRUE -``` + ```{r} # Create a folder for the output in the working directory. run_SSMSE_dir <- file.path("run_SSMSE-ex") @@ -199,7 +197,7 @@ run_SSMSE(scen_name_vec = c("H-ctl", "H-1"),# name of the scenario scope = "2", # to use the same recruitment devs across scenarios. impl_error_pattern = "none", # Don't use implementation error run_EM_last_yr = FALSE, # Run the EM in 106 - run_parallel = FALSE, + run_parallel = TRUE, sample_struct_list = sample_struct_list, # How to sample data for running the EM. seed = 12345) #Set a fixed integer seed that allows replication ``` diff --git a/README.md b/README.md index 07c15bc2..04069972 100644 --- a/README.md +++ b/README.md @@ -133,12 +133,10 @@ library(SSMSE) #load the package library(r4ss) #install using remotes::install_github("r4ss/r4ss@development) library(foreach) #if using run_parallel = TRUE library(doParallel) #if using run_parallel = TRUE +## Loading required package: iterators +## Loading required package: parallel ``` - ## Loading SSMSE - ## Loading required package: iterators - ## Loading required package: parallel - ``` r # Create a folder for the output in the working directory. run_SSMSE_dir <- file.path("run_SSMSE-ex") @@ -330,7 +328,7 @@ run_SSMSE(scen_name_vec = c("H-ctl", "H-1"),# name of the scenario scope = "2", # to use the same recruitment devs across scenarios. impl_error_pattern = "none", # Don't use implementation error run_EM_last_yr = FALSE, # Run the EM in 106 - run_parallel = FALSE, + run_parallel = TRUE, sample_struct_list = sample_struct_list, # How to sample data for running the EM. seed = 12345) #Set a fixed integer seed that allows replication ``` @@ -363,18 +361,9 @@ 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 library(tidyr) # use install.packages("tidyr") to install package if needed -## -## Attaching package: 'tidyr' -## The following object is masked from 'package:testthat': -## -## matches library(dplyr) ## ## Attaching package: 'dplyr' -## -## The following object is masked from 'package:testthat': -## -## matches ## The following objects are masked from 'package:stats': ## ## filter, lag