Package index • growthEstimation

All functions

Cod_CS_age_at_length: Example age_at_length data for Cod in the Celtic Sea.

Cod_CS_pars: Example parameter set for Cod in the Celtic Sea.

calculate_K(): Age-to-Ring Mapping Function Calculate_K(a) Deterministically maps true age to the expected annuli count, given a survey date, an annual ring-formation day, and a minimum age threshold.

calculate_and_aggregate_likelihood(): Calculate and Aggregate Signed Log-Likelihood Contributions

fit_tmb_nll(): Fit growth parameters by minimizing the negative log likelihood with TMB

generate_model_predictions_for_date(): Generate model predictions for a specific survey date

getGreens(): Calculate Green's function for fish abundance PDE

getLogLik(): Get log likelihood of age observations

plotAgeLikelihood(): Plot the likelihood of the observed age at length data

plot_log_likelihood(): Plot signed log-likelihood contributions with mean K lines

simulate_sample_from_model(): Simulate a sample from model predictions

solve_pde(): Numerically solve the PDE for fish abundance density

solve_thomas(): Solve a tridiagonal system of equations using the Thomas algorithm

spawning_density(): Spawning Density Function S(d)

tune_pars(): Interactively tune model parameters with a Shiny gadget

von_mises_pdf(): von Mises Probability Density Function