SSMSE package organization

SSMSE attempts to use functions that are as independent as possible (so that it is possible to write unit tests for any function), but are called within the wrapper functions in script runSSMSE.R (including run_SSMSE, run_SSMSE_scen, and run_SSMSE_iter).

SSMSE attempts to balance having too many R scripts (e.g., one per function) in the R subdirectory with having so few that the scripts are long and functions are impossible to find. Refactoring which script functions are found in may need to be reevaluated as the package grows. Here are descriptions of each of the scripts (as of 5/7/2020).

R script name	Description
calcF.R	Functions related to calculating fishing mortality.
checkinput.R	Check inputs to various functions in the package.
extendOM.R	Extend the OM beyond the initialization.
impl_error.R	Get or manipulate implementation error.
initOM.R	Initialize the OM.
manipulate_EM.R	Change the EM.
parse_MS.R	Get new catch from EM or proxy based on the management strategy.
recdevs.R	Get or manipulate recruitment deviations.
results.R	Get summarized output from the MSE analyses.
runSS.R	Run stock synthesis models.
runSSMSE.R	Run the high-level wrapper functions.
utils.R	Utility functions (e.g., move files, get generic values)

Note also that testthat scripts mirror the names of the scripts in the R subdirectory (e.g., functions in R script initOM.R are tested in the script test-init.OM.R.