Package index • marlin

All functions

Fish: R6 Class Representing a Fish Population
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: fishing metier (fleet–species interaction)
aggregate_yields(): Aggregate Per-Species Yield Outputs Into Fleet-Level Totals
allocate_effort(): Allocate fishing effort across patches
assign_ref_points(): Assign MSY-Based Reference Points to Each Species
assign_ssbmsy(): Find Baseline SSBmsy
calc_marginal_value(): Calculate Marginal Revenue and Marginal Profit by Patch and Fleet
clean_steps(): Clean Step Names from simmar Output
create_critter(): Create a Critter (Species) Object
create_fleet(): Create a Fleet Object
find_ancestors(): Find ancestors Ported fromhttps://github.com/James-Thorson-NOAA/FishLife/blob/main/R/Find_ancestors.R
find_msy(): Find MSY Referemce Points
find_neighbors(): Find 4-Neighbour (Rook) Adjacency Matrix for a Spatial Grid
fine_tune_costs(): Internal function to fine-tune cost parameters
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 Life History Traits from FishLife
go_fish(): Exploratory Fishing Step (No Population Effect)
marlin_pal(): marlin Colour Palettes
optimize_mpa(): Iteratively Optimise an MPA Network
plot_marlin(): Plot marlin Simulation Results
prep_movement(): Prepare Instantaneous Movement (Generator) Matrix
process_marlin(): Tidy Simulation Output from simmar
process_step(): Parse a Step Name into Year, Season, and Decimal Year
search_species(): Search FishLife Taxonomy for the Closest Species Match
sim_habitat(): Simulate Spatially Correlated Species Habitat
simmar(): Run the marlin Spatially Explicit Fisheries Simulation
theme_marlin(): ggplot2 Theme for marlin
tune_diffusion(): Tune Diffusion
tune_fleets(): Tune fleet parameters to match targets