All functions |
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Create matching column names across a list of data frames |
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Add short time varying parameter lines. At time of writing, this method will work for MG, selectivity, and catchability time varying, but not for SR |
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Calculate bias adjustment for recruitment deviations |
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Calculate fleets, years, and data types needed given sampling parameters |
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Calculate relative error |
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Change catch in the Stock Synthesis data list |
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Change composition data to dummy data for running the operating model |
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Change the bins for a composition object |
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Change the data that is available from a list object |
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Methods to alter the parameters estimated in a Stock Synthesis model |
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Change population and observed length-composition bins |
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Specify fishing mortality, \(F\), using the Stock Synthesis control file |
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Set the robustification constant for length-composition data |
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Methods to include parameters in a Stock Synthesis operating model |
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Set up population length bin structure |
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Adds or removes catchability parameters from a control file |
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Replace recruitment deviations |
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Change start year main recruitment deviations in control file |
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Alter a starter file for a retrospective analysis |
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Change start year of the data file |
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Replace tail compression value for length composition data |
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Methods to include time-varying parameters in a Stock Synthesis operating model |
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Change the years estimated |
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Check that the Stock Synthesis data file looks correct |
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Check input arguments for data |
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Check if input arguments have the same length |
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Check input forecast file values |
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Check if desired \(q\) parameters exist in control file list |
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Given sampling arguments, remove unneeded data from a .dat file |
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Control file for the cod estimation method |
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Control file for the cod operating model |
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Data for the cod operating model |
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Convert long-style ss3sim output to wide format |
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Copy the OM or EM into a scenario directory |
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Create an EM from an OM |
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Create the ss3sim logo |
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Helper function for building a ggplot facet |
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Fill in matrix across rows of weight-at-age data by interpolation |
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Find integer reference to fleet names |
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Get Stock Synthesis binary/executable location |
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Get summaries of fits to composition data from report file list |
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Get the folder location of an included Stock Synthesis model configuration |
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Get negative log likelihood (NLL) values from a report file list |
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Return a set of recruitment deviations |
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Extract Stock Synthesis simulation output |
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Extract time series from a model run with the associated standard deviation. |
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Get results for 1 iteration |
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Get results for 1 model run |
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Extract scalar quantities from a model run. |
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Extract Stock Synthesis simulation results for one scenario |
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Return the time series information from an iteration |
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Identify scenarios in |
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Get Variability About Recruitment Deviations (\(\sigma_R\)) |
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Determine if a Stock Synthesis run was successful |
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Make a list of lists with dataframe components into a dataframes |
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Plot results of a simulation as boxplots |
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Plot the cumulative mean for a parameter |
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Plot time-series values as lines |
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Plot results of a simulation as a scatterplot |
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Base plot for |
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Determine Fmsy for a given operating model |
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Replace a |
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Master function to run a set of simulations using ss3sim |
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Sample age compositions from a Stock Synthesis data file |
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Sample conditional age-at-length data |
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Sample the catches with observation error |
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Sample composition data from expected values |
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Sample the discard with observation error |
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Sample with a Dirichlet-Multinomial distribution |
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Sample the CPUE/index data with observation error |
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Sample length compositions from a Stock Synthesis data file |
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Sample observations using log-normal error corrected for bias |
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BETA VERSION Sample mean length (size-)-at-age data and write to file for use by the EM |
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Sample with a multinomial distribution |
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Sample empirical weight-at-age data |
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Example scalar data from the Introduction vignette |
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Set up bin structure for composition data |
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Setup parallel processing |
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Get scenario information from a data frame of specifications |
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Set up a generic scenario |
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Set up fleet-specific information |
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Create a named vector to look up full names for types of arguments |
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Create a name for an unnamed scenario |
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High-level wrapper to run a simulation |
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Check and standardize list components of sampling functions |
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Example time-series data from the Introduction vignette |
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Verify and standardize Stock Synthesis input files |
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Helper function for ensuring correct input for the plotting functions |