Package 'FIMS'

Title: The Fisheries Integrated Modeling System
Description: The Fisheries Integrated Modeling System is a next-generation framework of stock assessment models, assisting fishery managers with the goal of achieving sustainable fisheries. This system, when completed in a few years, offers the NOAA Fisheries and global fisheries science communities an advanced set of stock assessment models. These tools can be used separately or in combination to incorporate ecosystem and socioeconomic data and models, as well as climate effects and other drivers within the marine environment, into stock assessment models.
Authors: Christine Stawitz [aut, cre] , Nathan Vaughan [aut], Howard Townsend [aut], Ian G. Taylor [aut] , Matthew Supernaw [aut], Jane Sullivan [aut], Kyle Shertzer [aut] , Megumi Oshima [aut], Cole C. Monnahan [aut] , Timothy J. Miller [aut] , Richard Methot [aut], Patrick Lynch [aut] , Bai Li [aut] , Huihua Lee [aut], Christopher M. Legault [aut] , Kelli F. Johnson [aut] , James N. Ianelli [aut] , Alan Haynie [aut], Andrea M. Havron [aut] , Kathryn L. Doering [aut] , Edward J. Dick [aut] , Jon Brodziak [aut], Kristan Blackhart [aut], Peter Kuriyama [aut]
Maintainer: Christine Stawitz <[email protected]>
License: GPL (>= 3) | file LICENSE
Version: 0.2.0.0
Built: 2024-10-24 05:02:24 UTC
Source: https://github.com/noaa-fims/fims

Help Index

FIMS input data frame for milestone 1

Description

A dataset containing information necessary to run an age-structured stock assessment model in FIMS for milestone 1. This data was generated using the ASSAMC package written for the model comparison project.

Usage

data_mile1

Format

A data frame with 1140 observations of 8 variables:

type

The type of data the row contains. Allowed types include age, index, landings, and weight-at-age data.

name

A character string providing the name of the information source that the data was collected from, e.g., "Trawl fishery"

age

An integer age. Entry can be NA if information pertains to multiple ages, e.g., total catch rather than catch of age-4 fish.

datestart,dateend

Start and end dates of the data collection period. Format all dates using yyyy-mm-dd, which can accommodate fake years such as 0001-01-01.

value

The measurement of interest.

unit

A character string specifying the units of value. Allowed units for each data type are as follows. mt is used for index, landings, and weight-at-age data. number or proportion are each viable units for the composition data, where the former is the preferred unit of measurement.

uncertainty

A real value providing a measurement of uncertainty for value. For catches and survey indices of abundance this should be the standard deviation of the logged observations if you are using the lognormal distribution to fit your data. For composition data it will be your input sample size.

Source

www.github.com/Bai-Li-NOAA/Age_Structured_Stock_Assessment_Model_Comparison

Class constructors for FIMSFrame and associated child classes

Description

All constructor functions take a single input and build an object specific to the needs of each model type within FIMS. FIMSFrame is the parent class and the associated child classes have additional slots needed for each model type.

Usage

FIMSFrame(data)

Arguments

data

A data.frame that contains the necessary columns to construct a data frame of a given FIMSFrame-class.

Value

An object of the S4 class FIMSFrame or one of its child classes is validated and then returned. All objects will at a minimum have a slot called data to store the input data frame. Additional slots are dependent on the child class. Use showClass() to see all available slots.

Get the age-composition data to be used in the model

Description

Get the age-composition data to be used in the model

Usage

m_agecomp(x, fleet_name)

Arguments

x

The object containing the age-composition data.
fleet_name

The name of the fleet for the age-composition data.

Get the age-composition data data to be used in the model

Description

Get the age-composition data data to be used in the model

Usage

## S4 method for signature 'FIMSFrame'
m_agecomp(x, fleet_name)

Arguments

x

The FIMSFrame containing age-composition data.
fleet_name

The name of the fleet for the age-composition data.

Get the index data to be used in the model

Description

Get the index data to be used in the model

Usage

m_index(x, fleet_name)

Arguments

x

The object containing index.
fleet_name

The name of the fleet for the index data.

Get the index data to be used in the model

Description

Get the index data to be used in the model

Usage

## S4 method for signature 'FIMSFrame'
m_index(x, fleet_name)

Arguments

x

The FIMSFrame object containing index.
fleet_name

The name of the fleet for the index data.

Get the landings data to be used in the model

Description

Get the landings data to be used in the model

Usage

m_landings(x)

Arguments

x

The object containing landings.

Get the landings data to be used in the model

Description

Get the landings data to be used in the model

Usage

## S4 method for signature 'FIMSFrame'
m_landings(x)

Arguments

x

The FIMSFrame object containing landings.

Run the google test suite

Description

Intended for developers to run the google test suite from R.

Usage

run_gtest(...)

Arguments

...

Additional arguments to ⁠ctest --test-dir build⁠ such as "--rerun-failed --output-on-failure".

Setup and run the google test suite

Description

Intended for developers to set up their local environment and run the google test suite from R.

Usage

setup_and_run_gtest(...)

Arguments

...

Additional arguments to ⁠ctest --test-dir build⁠ such as "--rerun-failed --output-on-failure".

Set up your local environment to run the google tests locally

Description

Intended for developers to set up their local environment prior to running the integration tests.

Usage

setup_gtest()

Examples

## Not run: 
setup_gtest()

## End(Not run)