Package index • Rceattle

Data input / output

Read, write, build, and manipulate Rceattle data lists.

build_data(): Build an Rceattle data list in R
data_requirements(): Report which data inputs a model configuration requires
model_config(): Build a model-configuration slot for a data list
read_data(): Read a CEATTLE excel data file
write_data(): Write a data list to a CEATTLE xlsx workbook
write_template(): Write a minimal starter CEATTLE data workbook
clean_data(): Default-fill and tidy a data list before fitting
combine_data(): Combine two Rceattle data lists
rearrange_data() rearrange_dat(): Rearrange a data_list for TMB

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(): Specify the residual natural mortality (M1) model for Rceattle
build_growth(): Specify the growth model for Rceattle
build_srr(): Specify the stock-recruit relationship (SRR) for Rceattle
build_selectivity(): Selectivity specification
build_catchability(): Catchability specification
build_composition(): Composition-weighting specification
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

Run configuration

Save, load, and inspect the full model + estimation setup as a YAML run configuration.

save_config(): Save a model run configuration to a documented YAML file
load_config(): Load a model run configuration from a YAML file
run_config(): Extract the run configuration from a fit, data list, or config object

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(): Fit the CEATTLE assessment model
reweight_comps(): Iteratively reweight composition data (McAllister-Ianelli)
set_phases(): Default phasing order for CEATTLE parameters
TMBphase(): Run TMB with ADMB-style phased estimation
TMBAIC(): Calculate marginal AIC for a fitted model
model_average(): Model average of derived quantities
rename_output(): Label the derived quantities reported by a CEATTLE fit
parameter_dictionary(): Look up what a CEATTLE parameter is
parameter_index(): Locate every estimated parameter in the model's own coordinates
quantity_dictionary(): Look up what a CEATTLE reported quantity is
report_tables(): Assessment reporting tables from one or more Rceattle fits
standard_output(): Rceattle output in the NOAA standardized assessment format

Projections and MSE

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

run_mse(): Run a management strategy evaluation
load_mse(): Load saved MSE simulation runs
check_mse(): Check which saved MSE simulation files can be loaded
mse_summary(): Management strategy evaluation performance metric summary
remove_F(): Rerun with F = 0.
sample_rec(): Sample historical recruitment deviations into the projection

Diagnostics and simulation

Retrospective analysis, jitter testing, residual diagnostics, and simulation.

convergence_diagnostics(): Convergence diagnostics for a fitted Rceattle model
osa_residuals(): One-step-ahead (OSA) residuals for an Rceattle model
osa_diagnostics(): Statistical diagnostics for OSA residuals
process_residuals(): Process residuals for an Rceattle model's random-effect processes
retrospective(): Retrospective peels
jitter(): Jitter analysis
profile(<Rceattle>): Likelihood profile across one or more parameter cells
profile_components(): Likelihood components along a profile
self_test(): Self-test simulation analysis
sim_mod(): Simulate Rceattle data
simulate(<Rceattle>): Simulate data from a fitted Rceattle model
compare_sim(): Evaluate simulation performance
print(<Rceattle_retro>): Print method for a retrospective analysis
print(<Rceattle_jitter>): Print method for a jitter analysis
print(<Rceattle_selftest>): Print method for a self-test
print(<Rceattle_profile>): Print method for a likelihood profile
print(<Rceattle_mse_summary>): Print method for an MSE summary

Diagnostics — shared arguments

The common vocabulary retrospective(), jitter() and self_test() share: object, cores and fit_control, and what fit_control() reaches through a refit.

rceattle-refit-args: Shared refit-diagnostic arguments

Plotting — shared arguments

The common vocabulary the timeseries, predation and selectivity plotters share: line_col, lwd, lty, alpha, species, spnames, minyr/maxyr, incl_proj, incl_mean, add_ci and model_names.

rceattle-plot-args: Shared plotting arguments

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_ssb_depletion(): Plot SSB depletion
plot_exploitable_biomass(): Plot exploitable biomass

Plotting — fishing and natural mortality

Visualize fishing mortality, catch, and total mortality.

plot_catch(): Fishery catch fits
plot_f(): plot F
plot_mortality(): Plot M1 or M2 at age
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(): Survey index fits
plot_index_residual(): Survey index residuals
plot_catchability(): Survey catchability over time
plot_comp(): Plot composition fits and residuals
plot_profile(): Plot the likelihood components across a profile
plot(<Rceattle_profile>): Plot method for a likelihood profile
plot(<rceattle_osa>): Plot one-step-ahead (OSA) residual diagnostics
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 by predation
plot_b_eaten_prop(): Plot biomass consumed of each prey species by predator
plot_diet_comp(): Plot diet composition fits
plot_diet_comp1(): Plot diet composition fits (bubble/grid diagnostic)
plot_diet_comp2(): Plot diet composition fits (aggregation-aware)
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
print(<summary.Rceattle>): Print method for an Rceattle model summary
print(<Rceattle_data>) summary(<Rceattle_data>): Print method for an Rceattle data list
print(<rceattle_report>): Print method for a set of assessment reporting tables
switch_check(): Function to check for missing switches for map and parameter functions
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.
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>): 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

Deprecated

Superseded functions kept for backward compatibility. They still work but emit a deprecation message; use the named replacement in new code.

plot_logindex(): Survey index fits on the log scale (deprecated)
plot_depletionSSB(): Plot SSB depletion (deprecated name)
plot_indexresidual(): Plot survey index residuals (deprecated name)