Function reference • FLOSS

App and guides

run_app(): Start the FLOSS app

floss_guide(): Copy, and optionally render, a FLOSS guide

floss_tip(): Short explanations of FLOSS settings

Fishery

fishery() validate_fishery() fishery_years(): Define a fishery

effort_trend(): Effort trend for one fleet

reef_fishery(): The three-fleet reef fishery used in the examples

one_gear_fishery(): One-gear fishery with constant (or stepped) F/Fmsy

trend_values(): Deterministic effort trend values

effort_sim(): Simulate fleet effort

load_fishery(): Example fishery shipped with the package

Species

species() validate_species(): Define a species

selectivity(): Selectivity-at-length for one fleet

one_gear_species(): Adapt a species to a one-gear fishery

species_library() load_species() save_species() delete_species(): Species library

write_spec() read_spec(): Write and read FLOSS specs as YAML

species_lhpar(): Life-history FLPar for FLife

species_sel(): Selectivity-at-length and -at-age by fleet

Operating model

build_om(): Build a stochastic operating model for one species

build_oms(): Build operating models for several species sharing one fishery

calibrate_msy(): Equilibrium calibrated to a target MSY

catch_fleet(): True catch by fleet

plot_om(): Plot stock status of an operating model

plot_fleets(): Plot apical fishing mortality or catch by fleet

plot_effort(): Plot fleet effort

Dynamics

plot_eq(): Equilibrium curves with the realised trajectory

plot_srr(): Stock-recruitment curve with simulated pairs

plot_eq_selectivity(): Equilibrium curves under alternative selectivities

plot_ssb_vb(): Spawning biomass versus vulnerable biomass by fleet

Treatments

treatment(): Define a treatment

run_treatment(): Run a baseline and treatments with common random numbers

plot_treatment(): Plot the response to treatments

Sampling

oem_settings(): Sampling settings

survey_settings(): Survey settings

season_design(): Seasonal sampling design

reef_oem(): Sampling settings of the reef example

sample_data() sample_catch() sample_effort() sample_cpue() sample_survey() sample_lfd() sample_bio(): Generate observed data

planted_artefacts(): Artefacts planted in the sampling settings and the fishery

floss_gears(): FLRef gear objects for an operating model

lfd_annual(): Pool seasonal length samples into annual ones

Observations and size data

plot_availability(): Plot which data exist for which years

plot_obs(): Plot observed catch, CPUE and survey indices

plot_lfd(): Plot length samples

plot_seasons(): Seasonal length sampling: sample sizes and mean length by season

plot_bio(): Plot biological samples (observations only)

alk_obs(): Observed age-length key

caa_obs(): Catch-at-age from length samples and an age-length key

plot_caa(): Plot catch-at-age from caa_obs()

length_indicators(): Length-based indicators by year and source

plot_length_indicators(): Plot length-based indicators

plot_indicators(): Indicator dashboard

Aggregation (teaching)

catch_table() effort_table() nominal_cpue(): Catch, effort and nominal CPUE: by fleet or aggregated

lfd_aggregate(): Length samples: by fleet or pooled, as sampled or raised to the catch

plot_aggregate(): Plot catch, effort or nominal CPUE by fleet or aggregated

Basic fits (optional)

fit_growth(): Fit von Bertalanffy growth to observed length-at-age

fit_lw(): Fit the length-weight relationship

fit_maturity(): Fit a logistic maturity ogive

catch_curve(): Age-based catch curve

catch_curve_length(): Length-converted catch curve and selectivity

M_empirical(): Empirical natural mortality estimators

cpue_check(): Check the CPUE assumptions against the truth (trainers)

plot_fit(): Plot a basic fit

Truth and export

status_table(): True stock status

plot_truth(): Plot true status trajectories

plot_kobe(): Kobe plot of true status

export_truth(): Download the truth (trainers)

export_data(): Export datasets for trainees

read_dataset(): Read an exported dataset

simulate_fishery(): Simulate a fishery and its data in one call

as_flr(): FLR objects for JABBA3 and FLicc

Colours

floss.r4col(): FLOSS colour palette (r4ss colours, as in JABBA)