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ss3sim (version 0.9.0)

Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description

The ss3sim package develops a framework for fisheries stock assessment simulation testing with Stock Synthesis 3 (SS3).

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Version

Install

install.packages('ss3sim')

Monthly Downloads

520

Version

0.9.0

License

MIT + file LICENSE

Maintainer

Sean Anderson

Last Published

December 24th, 2015

Functions in ss3sim (0.9.0)

add_nulls

Add NULL values to non-existent list elements

run_bias_ss3

Determine level of bias adjustment for SS3 runs

get_recdevs

Return a set of recruitment deviations

sample_mlacomp

[BETA VERSION] Sample mean length (size-)-at-age data and write to file for use by the EM.

get_model_folder

Get the folder location of an included SS3 model configuration

expand_scenarios

Create vectors of scenario IDs

change_tv

Methods to include time-varying parameters in an SS3 operating model

ts_dat

Example time series data from the ss3sim vignette

calculate_data_units

Given sampling arguments, calculate super set of fleets, years, and data types.

change_agecomp

(Depreciated) Sample age compositions from expected values

change_tail_compression

Replace tail compression value for length composition data.

verify_input

Verify and standardize SS3 input files

ss3sim

ss3sim: Fisheries stock assessment simulation testing with Stock Synthesis

verify_plot_arguments

A helper function to check the correct input for the plotting functions.

id_scenarios

Identify ss3sim scenarios within a directory

check_data

Check that the SS3 data file looks correct

get_results_scenario

Extract SS3 simulation results for one scenario.

change_e

Methods to alter which parameters are estimated in a SS3 .ctl file.

change_year

Methods to change the years in an ss3sim model

plot_ts_boxplot

Plot timeseries values as boxplots.

create_argfiles

Create template argument input files

cleanup_ss3

Clean up after an SS3 run

change_em_binning

Change population and observed length composition bins in an SS estimation model

case_index

Write a case file for index data to the disk.

change_lcomp

(Depreciated) Sample length compositions from expected values

vbgf_func

Predict length given VBGF parameters

plot_scalar_points

Plot scalar values as points.

profile_fmsy

Determine Fmsy for a given operating model

get_bin

Get SS3 binary/executable location in package

change_fltname

Standardize column name for FltSvy in event r4ss is not the newest version.

case_fishing

Write a case file for fishing data to the disk.

change_rec_devs

Replace recruitment deviations

get_args

Take a csv file, read it, and turn the first column into the list names and the second column into the list values.

case_deparse

Turn an argument describing an object into a character.

fill_across

Fill in matrix across rows of weight-at-age data by interpolation

pastef

Paste with "/" as the separator

get_bin_info

Get the parameter values for change_bin

calculate_re

Calculate relative error

sample_wtatage

Sample empirial weight-at-age data and write to file for use by the EM

copy_ss3models

Copy the operating and estimation models and create a folder structure

plot_scalar_boxplot

Print scalar values as boxplots.

get_results_derived

Extract time series from a model run with the associated standard deviation.

scalar_dat

Example scalar data from the ss3sim vignette

get_caseval

Take a scenario ID and a case type and return the case number

extract_expected_data

Extract the expected data values

substr_r

Substring from right

ss3sim_base

Base wrapper function to run an ss3sim simulation

sanitize_admb_options

Check admb options to make sure there aren't flags there shouldn't be

get_results_all

Extract SS3 simulation output

case_tv

Write time varying casefiles to the disk

get_sigmar

Get recruitment deviation sigma

plot_ts_lines

Plot timeseries values as lines.

run_ss3sim

Master function to run SS3 simulations

change_index

(Depreciated) Sample the biomass with observation error

rename_ss3_files

Rename SS3-version-specific files

change_f

Alter the fishing mortality (F) values in an SS3 .par file.

sample_lcomp

Sample length compositions from expected values

clean_data

Given sampling arguments remove ("clean") all data in a .dat file that is not specified

calculate_runtime

Calculate run time

get_results_timeseries

Extract time series from a model run.

change_retro

Alter a starter file for a retrospective analysis

sample_index

Sample the biomass with observation error

case_comp

Write a case file for length- or age-composition data

change_maturity

Alter a control file to specify the SS3 maturity option

change_data

Change the data that is available as output from an SS operating model.

facet_form

A helper function for building a ggplot facet. Used internally by the plotting functions.

get_results_scalar

Extract scalar quantities from a model run.

setup_parallel

Setup parallel processing

change_lcomp_constant

Set the robustification constant for length composition data.

get_fish600_casefolder

Get the folder location of the FISH600 case files

sample_calcomp

Sample conditional age-at-length (CAL) data and write to file for use by the EM.

plot_ts_points

Plot timeseries values as points.

get_caseargs

Take a scenario ID and return argument lists

run_ss3model

Run an operating or estimation model for a specified set of scenario IDs

standardize_bounds

Standardize the bounds of the estimation model control file.

bias_ss3

Perform a single bias adjustment run

get_nll_components

Get negative log likelihood (NLL) values from a report file list

sample_agecomp

Sample age compositions from expected values