gadgetSim: gadgetSim: A package for creating simulated datasets from...

In inspktrgadget/gadgetSim: Create Gadget replicates for use in simulation studies

Description

gadgetSim takes output from a Gadget model and formats it so that the output can be used as an operating model for simulation purposes (e.g. using Gadget as an estimation model). The core of the package uses a handful of functions which can be found at gadget_simulate. Mainly, the package takes output from the Gadget StockStdPrinter printfile component, creates a simulated population based on the mean length and standard deviation, and then samples this simulated population based on various selectivity and age-length sampling specifications. The sampled output can then be used as data in an estimation model.

gadgetSim takes output from a Gadget model and formats it so that the output can be used as an operating model for simulation purposes (e.g. using Gadget as an estimation model). The core of the package uses a handful of functions which can be found at gadget_simulate. Mainly, the package takes output from the Gadget StockStdPrinter printfile component, creates a simulated population based on the mean length and standard deviation, and then samples this simulated population based on various selectivity and age-length sampling specifications. The sampled output can then be used as data in an estimation model.

Gadget Simulation functions

These functions use the output from get_stock_std and are meant to be used in conjunction with each other. add_lengthgroups takes the output from get_stock_std and distributes the number at each year, step, area, and age combination around its mean length using the standard deviation computed by Gadget. The data.frame value returned by this function is not very useful by itself, but instead is meant to be fed to survey_gadget, which samples the data using a selectivity curve and adding multiplicative error to the numbers. This produces a simulated sample of Gadget output. This sample can be further sub-sampled for length and age data using strip_age_length_data according to the given length and age proportions. Note that the length and age proportions are hierarchical in this function, which is intentional as an effort to produce more realistic sampling of composition data. The age proportion value is itself a subset of the length proportion value. For example, if 0.2 of the data are sampled for length, and 0.2 of those data are sampled for age, then the proportion of all the data sampled for age is 0.2 * 0.2 = 0.04.

These functions use the output from get_stock_std and are meant to be used in conjunction with each other. add_lengthgroups takes the output from get_stock_std and distributes the number at each year, step, area, and age combination around its mean length using the standard deviation computed by Gadget. The data.frame value returned by this function is not very useful by itself, but instead is meant to be fed to survey_gadget, which samples the data using a selectivity curve and adding multiplicative error to the numbers. This produces a simulated sample of Gadget output. This sample can be further sub-sampled for length and age data using strip_age_length_data according to the given length and age proportions. Note that the length and age proportions are hierarchical in this function, which is intentional as an effort to produce more realistic sampling of composition data. The age proportion value is itself a subset of the length proportion value. For example, if 0.2 of the data are sampled for length, and 0.2 of those data are sampled for age, then the proportion of all the data sampled for age is 0.2 * 0.2 = 0.04.

Retrieving StockStdPrinter output

The main function to retrieve StockStdPrinter output is get_stock_std. This produces a printfile given the arguments and calls Gadget using this printfile to produce standard stock output. This output is what is then used to re-create a simulated population using the functions above. gadgetSim is designed to work with and around the Rgadget package as much as possible; therefore, this function also checks to see if a user has this package installed, and, if so, and gadget.fit has been called will take the StockStdPrinter output created by Rgadget

The main function to retrieve StockStdPrinter output is get_stock_std. This produces a printfile given the arguments and calls Gadget using this printfile to produce standard stock output. This output is what is then used to re-create a simulated population using the functions above. gadgetSim is designed to work with and around the Rgadget package as much as possible; therefore, this function also checks to see if a user has this package installed, and, if so, and gadget.fit has been called will take the StockStdPrinter output created by Rgadget

Functions to call Gadget

There is a single function used to call Gadget on the command line, which is call_gadget. This function is very similar to callGadget in the Rgadget package. The key difference is that an optional path can be specified to call_gadget, which allows the function to be called on a Gadget model from any working directory.

There is a single function used to call Gadget on the command line, which is call_gadget. This function is very similar to callGadget in the Rgadget package. The key difference is that an optional path can be specified to call_gadget, which allows the function to be called on a Gadget model from any working directory.

Read Gadget files

There are several various functions to read different Gadget files. These are mostly used internally, but are exported for convenience to the user if their use is ever desired. These functions also contain an optional path argument to call the functions from any working directory see ?read_gadget_*, where * is the Gadget filetype desired to read (i.e. main). These fucntions also attempt to replicate Rgadget output as much as possible. The structure and classes from this output are similar to that of the synonymous functions in Rgadget.

There are several various functions to read different Gadget files. These are mostly used internally, but are exported for convenience to the user if their use is ever desired. These functions also contain an optional path argument to call the functions from any working directory see ?read_gadget_*, where * is the Gadget filetype desired to read (i.e. main). These fucntions also attempt to replicate Rgadget output as much as possible. The structure and classes from this output are similar to that of the synonymous functions in Rgadget.

Author(s)

Paul Frater

Maintainer: Paul Frater <[e-mail]>

inspktrgadget/gadgetSim documentation built on May 10, 2019, 9:51 a.m.