Package index
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Cod_CS_age_at_length - Example age_at_length data for Cod in the Celtic Sea.
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Cod_CS_pars - Example parameter set for Cod in the Celtic Sea.
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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.
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calculate_and_aggregate_likelihood() - Calculate and Aggregate Signed Log-Likelihood Contributions
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fit_tmb_nll() - Fit growth parameters by minimizing the negative log likelihood with TMB
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generate_model_predictions_for_date() - Generate model predictions for a specific survey date
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getGreens() - Calculate Green's function for fish abundance PDE
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getLogLik() - Get log likelihood of age observations
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getNumberDensity() - Get number density as a function of length and time
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getPeriodicNumberDensity() - Get periodic number density as a function of length and time
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plotAgeLikelihood() - Plot the likelihood of the observed age at length data
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plotDensity2D() - Plot density function snapshots at yearly intervals
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plotDensity3D() - Plot density function as an interactive 3D surface
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plot_log_likelihood() - Plot signed log-likelihood contributions with mean K lines
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simulate_sample_from_model() - Simulate a sample from model predictions
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solve_pde() - Numerically solve the PDE for fish abundance density
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solve_thomas() - Solve a tridiagonal system of equations using the Thomas algorithm
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spawning_density() - Spawning Density Function S(d)
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tune_pars() - Interactively tune model parameters with a Shiny gadget
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von_mises_pdf() - von Mises Probability Density Function