Package index • marlin

All functions

Fish: R6 Class Representing a Fish

FishBase_and_RAM: Database of stock-recruit, population-dynamics, size, growth, maturity, and mortality parameters. Pull Pulled from Thorson's FishLife package on 2022/03/06, as loading FishLife itself generated far too many dependencies. Will consider fix at later date

Metier: R6 Class Representing a fishing fleet

assign_ref_points(): Assign References Points

assign_ssbmsy(): Find Baseline SSBmsy

clean_steps(): A small function to trim any characters from step names in the output of marlin::simmar

create_critter(): Create Critter

create_fleet(): Create Fleet

find_ancestors(): Find ancestors Ported fromhttps://github.com/James-Thorson-NOAA/FishLife/blob/main/R/Find_ancestors.R

find_msy(): Find MSY Referemce Points

fine_tune_costs(): Internal function to fine-tune cost parameters

fleet_tuner(): fleet tuner

generate_length_at_age_key(): generate_length_to_age_key

get_distance_to_mpas(): Measures the distance of each cell to the nearest MPA edge and to all MPA cells

get_traits(): Get Traits

marlin_pal(): marlin pal palette

optimize_mpa(): Optimize MPA network

plot_marlin(): Plot Marlin generates time series, spatial, or length composition plots from marlin run

prep_movement(): Prepare movement matrix

process_marlin(): Process Marlin

process_step(): Process Step Convert step_YEAR_SEASON notation into YEAR_SEASON, YEAR, and SEASON

quota_finder(): Title

search_species(): Search species: Ported from https://github.com/James-Thorson-NOAA/FishLife/blob/main/R/Search_species.R

sim_habitat(): Simulate species habitats with correlations across space and among species

simmar(): simmar is the wrapper function for the marlin package

theme_marlin(): ggplot2 theme for marlin

tune_fleets(): tune_fleets tunes parameters of the fleet model to achieve desired initial conditions. note that this is not exact: post-tuning values will not perfectly match inputs since for example some tuning steps depend on prior tuning step, making it difficult to tune everything at once.