Package index • FIMS

Data

FIMS comes with a selection of built-in datasets that are used in examples to illustrate various visualization challenges.

data1: FIMS input data frame

Run FIMS

Primary functions used when setting up or running a FIMS model.

FIMSFrame(): Class constructors for FIMSFrame and associated child classes

get_data() get_fleets() get_n_fleets() get_n_years() get_start_year() get_end_year() get_ages() get_n_ages() get_lengths() get_n_lengths(): Get a slot in a FIMSFrame object

m_landings() m_index() m_agecomp() m_lengthcomp() m_weight_at_age() m_age_to_length_conversion(): Get a vector of data to be passed to a FIMS module from a FIMSFrame object

create_default_parameters() update_parameters(): Create default parameters for a FIMS model

initialize_data_distribution() initialize_process_distribution() initialize_process_structure(): Set up a new distribution for a data type or a process

lognormal() multinomial(): Distributions not available in the stats package

initialize_fims(): Initialize FIMS modules

FIMSFit(): Class constructors for class FIMSFit and associated child classes

fit_fims(): Fit a FIMS model (BETA)

get_input() get_report() get_obj() get_opt() get_max_gradient() get_sdreport() get_estimates() get_fits() get_number_of_parameters() get_timing() get_version(): Get a slot in a FIMSFit object

is.FIMSFit(): Check if an object is of class FIMSFit

is.FIMSFits(): Check if an object is a list of FIMSFit objects

is_fims_verbose(): Should FIMS be verbose?

Package development

Primary functions used when developing FIMS package.

check_fims(): Run all styling, documentation, and testing for FIMS repository

remove_test_data(): Remove test data

run_gtest(): Run the google test suite

run_r_integration_tests(): Run R integration tests

run_r_unit_tests(): Run R unit tests

setup_and_run_gtest(): Setup and run the google test suite

setup_gtest(): Set up your local environment to run the google tests locally

style_cpp(): Style the C++ files

Ops(<Rcpp_Parameter>,<Rcpp_Parameter>) Ops(<Rcpp_Parameter>,<numeric>) Ops(<numeric>,<Rcpp_Parameter>) Ops(<Rcpp_ParameterVector>,<Rcpp_ParameterVector>) Ops(<Rcpp_ParameterVector>,<numeric>) Ops(<numeric>,<Rcpp_ParameterVector>) Math(<Rcpp_ParameterVector>): Sets methods for operators under the S4 Generic Group, Ops

`[<-`(<Rcpp_ParameterVector>,<ANY>,<ANY>,<ANY>) `[`(<Rcpp_ParameterVector>,<numeric>,<ANY>,<ANY>) length(<Rcpp_ParameterVector>) sum(<Rcpp_ParameterVector>) dim(<Rcpp_ParameterVector>) Summary(<Rcpp_ParameterVector>): Setter for Rcpp_ParameterVector

use_testthat_template(): Create tests/testthat/test-*.R test file

reshape_json_derived_quantities(): Reshape JSON derived quantities

reshape_json_estimates(): Reshape JSON estimates

reshape_json_fits(): Reshape JSON 'fits' components

reshape_json_values(): Reshape JSON 'values' components

reshape_tmb_estimates(): Reshape TMB estimates