Package index • Rceattle

Data input / output

Read, write, and manipulate Rceattle data lists.

read_data(): Read a CEATTLE excel data file
write_data(): Write data file
clean_data(): Function to clean data prior to Rceattle runs
combine_data(): Combine data sets. Will use the env_data data set from data_set1 and diet data will have to be updated.
rearrange_dat(): Rearrange
data_check(): Function to check data for errors. Does not update the data set!

Model setup

Build parameter lists, map objects, bounds, and biological inputs.

build_params(): Build parameter list from cpp file
build_map(): Main function to construct the TMB map argument for CEATTLE
build_bounds(): Build parameter bounds
build_M1(): Define M1 specifications
build_growth(): Specify the growth model for Rceattle
build_srr(): Specify the stock-recruit relationship (SRR) for Rceattle
build_hcr(): Specify the harvest control rule (HCR) used for Rceattle
build_hcr_map(): Function to construct the TMB map argument for CEATTLE for projecting under alternative harvest control rules
fit_control(): Bundle the optimizer / sdreport / phasing controls for fit_mod()
linkage_spec(): Capture a linkage specification

Map helpers

Low-level helpers called by build_map() to configure parameter estimation.

adjust_map_shared_params(): Helper to adjust map for shared catchability/selectivity indices
build_map_catchability(): Helper to set map for Catchability parameters
build_map_debug(): Helper to set map for debug mode
build_map_f_and_data_weights(): Helper to set map for Fishing Mortality and Data Weights
build_map_fixed_natage(): Helper to set map for Fixed N-at-Age models
build_map_growth(): Helper to set map for growth parameters
build_map_m1(): Helper to set map for Natural Mortality (M1) parameters
build_map_predation(): Helper to set map for Predation Mortality (M2) parameters
build_map_recruitment(): Helper to set map for Recruitment parameters
build_map_selectivity(): Helper to set map for Selectivity parameters

Model fitting

Fit single- or multi-species CEATTLE models and manage output.

fit_mod(): This function runs CEATTLE
set_phases(): Function to set phasing order
TMBphase(): Run TMB using phases
TMBAIC(): Calculate marginal AIC for a fitted model
model_average(): Model average of derived quantities
rename_output(): Function to rename derived quantities from Rceattle

Projections and MSE

Forward projections under alternative harvest strategies and closed-loop management strategy evaluation.

run_mse(): Run a management strategy evaluation
load_mse(): Function to load .RDs files from MSE runs
check_mse(): Function to load .RDs files from MSE runs
mse_summary(): Management strategy evaluation performance metric summary
remove_F(): Rerun with F = 0.
sample_rec(): Sample historical recruitment deviates and place in the projection

Diagnostics and simulation

Retrospective analysis, jitter testing, and simulation.

retrospective(): Retrospective peels
jitter(): Jitter analysis
sim_mod(): Simulate Rceattle data
compare_sim(): Evaluate simulation performance

Data weighting

Composition data reweighting methods.

calc_mcall_ianelli(): Function to calculate McAllister-Ianelli weights
calc_mcall_ianelli_diet(): Function to calculate McAllister-Ianelli weights for diet data
check_composition_data(): Check and Clean Composition Data
check_caal_data(): Check and Clean CAAL Data

Plotting — population dynamics

Visualize biomass, recruitment, SSB, and depletion trajectories.

plot_timeseries(): Plot time-series
plot_biomass(): Plot biomass
plot_ssb(): Plot spawning stock biomass (SSB)
plot_recruitment(): Plot recruitment
plot_depletion(): Plot biomass depletion
plot_depletionSSB(): Plot SSB depletion
plot_exploitable_biomass(): Plot exploitable biomass
plot_ssb_depletion(): Plot SSB depletion (deprecated name)

Plotting — fishing and natural mortality

Visualize fishing mortality, catch, and total mortality.

plot_catch(): Landings fits
plot_f(): plot F
plot_mortality(): Plot M1 + M2
plot_m_at_age(): Plot natural mortality by age
plot_m2_at_age_prop(): Plot predation mortality by age and predator

Plotting — surveys and fit

Visualize survey indices, fits, and residuals.

plot_index(): CPUE fits
plot_logindex(): log(CPUE) fits
plot_indexresidual(): CPUE residual
plot_comp(): Plot time series of comp data
plot_data(): Timeline of data used in the model likelihoods
plot_form(): Plot functional form

Plotting — predation and diet

Visualize predation mortality, rations, and diet composition.

plot_b_eaten(): Plot biomass eaten
plot_b_eaten_prop(): Plot biomass consumed of each prey species by predator
plot_diet_comp(): Plot diet composition fits
plot_ration(): Plot ration

Plotting — biology

Visualize selectivity, maturity, and stock-recruitment.

plot_selectivity(): Plot selectivity
plot_selectivity_vs_maturity(): Plot fishery selectivity and maturity
plot_maturity(): Plot maturity
plot_stock_recruit(): Plot stock recruit function

Example datasets

Built-in data lists for the Bering Sea (BS), Gulf of Alaska (GOA), Georges Bank, and other applications.

BS2017SS: Data inputs for single species CEATTLE of the Bering Sea from 1979 to 2017
BS2017MS: Data inputs for multispecies CEATTLE of the Bering Sea from 1979 to 2017
EBS_ss_run: Fitted single-species CEATTLE model for the Eastern Bering Sea
EBS_ss_M_run: Fitted single-species CEATTLE model with estimated M for the Eastern Bering Sea
EBS_ms_run: Fitted multispecies CEATTLE model for the Eastern Bering Sea
GOA2018SS: Data inputs for a single-species Gulf of Alaska CEATTLE model (2018)
GOApollock: Data inputs for Gulf of Alaska walleye pollock CEATTLE model
GOAsafe2018: Gulf of Alaska 2018 SAFE report reference values
GOAatf: Data inputs for Gulf of Alaska arrowtooth flounder CEATTLE model
GOAatf2023: Data inputs for Gulf of Alaska arrowtooth flounder CEATTLE model (2023)
GOAcod: Data inputs for Gulf of Alaska Pacific cod CEATTLE model
GeorgesBank3spp: Data inputs for a three-species Georges Bank CEATTLE model
NorthernRockfish2022: Data inputs for Northern Rockfish CEATTLE model (2022)
Atka2022: Data inputs for Atka mackerel CEATTLE model (2022)
whamGrowthData: Data inputs for CEATTLE model with WHAM-estimated growth

Miscellaneous

S3 methods, utility functions, and internal helpers.

print(<Rceattle>): Print method for fitted Rceattle models
summary(<Rceattle>): Compact summary method for Rceattle fits
switch_check(): Function to check for missing switches for map and parameter functions
convert_switches(): Convert intuitive text strings to integer switches for TMB
revert_switches(): Convert integer switches to intuitive text strings. Maintains backwards compatability.
get_growth_matrix_r(): Generate Length-at-Age Transition Matrix
get_weight_at_age_r(): Calculate Predicted Weight-at-Age
rich.colors.short(): Make a vector of colors.
t_col(): #https://www.dataanalytics.org.uk/make-transparent-colors-in-r/
as.data.frame(<Rceattle>): Tidy long-format derived quantities from an Rceattle fit
coef(<Rceattle>): Extract estimated parameters from an Rceattle fit
logLik(<Rceattle>): Log-likelihood of an Rceattle fit
plot(<Rceattle>): Plot method for fitted Rceattle models
residuals(<Rceattle>): Observed-vs-fitted residuals from an Rceattle fit
vcov(<Rceattle>): Variance-covariance matrix for an Rceattle fit
prior_beta(): Beta prior on a linkage coefficient
prior_gamma(): Gamma prior on a linkage coefficient
prior_lognormal(): Lognormal prior on a linkage coefficient
prior_normal(): Normal prior on a linkage coefficient
validate_switches(): Validates switches are correct