Fisheries Stock Assessment Simulation Testing with Stock Synthesis
Create matching column names across a list of data frames
Add a q setup line into an SS control file
Add NULL values to non-existent list elements
Add short time varying parameter lines. At time of writing, this metho...
Given sampling arguments, calculate super set of fleets, years, and da...
Calculate relative error
Write a case file for length- or age-composition data
Turn an argument describing an object into a character.
Write a case file for fishing data to the disk.
Write a case file for index data to the disk.
Write time varying casefiles to the disk
Change the data that is available as output from an SS operating model...
Methods to alter which parameters are estimated in a SS3 .ctl file.
Check and change forecast file years if necessary
Change population and observed length composition bins in an SS estima...
Alter fishing mortality (F) using the SS control file
Alter the fishing mortality (F) values in an SS3 .par file.
Set the robustification constant for length composition data.
Methods to include parameters in an SS3operating model
Set up population length bin structure
Replace recruitment deviations
Replace recruitment deviations
Alter a starter file for a retrospective analysis
Replace tail compression value for length composition data.
Methods to include time-varying parameters in an SS3 operating model
Check that the SS data file looks correct
Check input arguments for data
Given sampling arguments remove ("clean") all data in a .dat file that...
Clean up after an SS3 run
Copy the operating and estimation models and create a folder structure
Create template argument input files
Create vectors of scenario IDs
A helper function for building a ggplot facet. Used internally by the ...
Fill in matrix across rows of weight-at-age data by interpolation
Take a csv file, read it, and turn the first column into the list name...
Get SS3 binary/executable location in package
Get the parameter values for change_bin
Take a scenario ID and return argument lists
Take a scenario ID and a case type and return the case number
Get the folder location of the FISH600 case files
Get the folder location of an included SS3 model configuration
Get negative log likelihood (NLL) values from a report file list
Return a set of recruitment deviations
Extract SS3 simulation output
Extract time series from a model run with the associated standard devi...
Extract scalar quantities from a model run.
Extract SS3 simulation results for one scenario.
Extract time series from a model run.
Get Variability About Recruitment Deviations ()
Get the ss version (either 3.24 or 3.30) from a dat_list list.
Get the ss version (either 3.24 or 3.30) from an ss file
Identify ss3sim scenarios within a directory
Print scalar values as boxplots.
Plot scalar values as points.
Plot timeseries values as boxplots.
Plot timeseries values as lines.
Plot timeseries values as points.
Determine Fmsy for a given operating model
Remove a q setup line into an SS control file
Remove a q setup line into an SS control file only
Rename SS3-version-specific files
Run an operating or estimation model for a specified set of scenario I...
Master function to run SS3 simulations
Sample age compositions from a Stock Synthesis data file
Sample conditional age-at-length (CAL) data and write to file for use ...
Sample composition data from expected values
Sample the biomass with observation error
Sample length compositions from a Stock Synthesis data file
[BETA VERSION] Sample mean length (size-)-at-age data and write to fil...
Sample empirical weight-at-age data and write to file for use by the E...
Check admb options to make sure there aren't flags there shouldn't be
Setup parallel processing
ss3sim: Fisheries stock assessment simulation testing with Stock Synth...
Base wrapper function to run an ss3sim simulation
Standardize the bounds of the estimation model control file.
Substring from right
Predict length given VBGF parameters
Verify and standardize SS3 input files
A helper function to check the correct input for the plotting function...
Develops a framework for fisheries stock assessment simulation testing with Stock Synthesis (SS) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.