Package index • MARS

Data

S4 objects for data setup.

MARSdata-class: MARSdata S4 object

Model setup

Prepare the data and parameters, then run the model.

check_data(): Check dimensions and inputs in MARSdata object

make_parameters() make_map() check_parameters(): Make list of parameters for RTMB

prior_h() prior_M() prior_q(): Priors for MARS model

fit_MARS(): Fit MARS model

MARSassess-class: MARSassess S4 object

Model evaluation

Evaluate model fit and run diagnostics.

profile(<MARSassess>) plot(<MARSprof>): Profile parameters of MARS model

report(): Generate markdown reports

residuals(<MARSassess>): Calculate model residuals

retrospective() plot(<MARSretro>) summary(<MARSretro>) report(<MARSretro>): Retrospective analysis

simulate(<MARSassess>): Simulate data

Population dynamics

Functions used in the population model.

calc_F(): Newton-Raphson search for fishing mortality

calc_POP() calc_HSP(): Predict the probability of CKMR kinship pairs

calc_index(): Calculate index at age

calc_nextN(): Project stock abundance to the next time step

calc_phi_project(): Equilibrium spawners per recruit by projection

calc_phi_simple() calc_NPR(): Simple spawners per recruit calculation

calc_population(): Multi-fleet, multi-area, multi-stock population dynamics model

calc_recruitment(): Calculate recruitment from stock-recruit function

conv_mov(): Calculate movement matrix for all age classes

conv_selpar() calc_sel_len() calc_fsel_age() calc_isel_age(): Selectivity at age and length

calc_eqdist(): Equilibrium distribution from movement matrix

Likelihood and prior functions

Calculate the log-likelihood or log-prior density functions from data and estimated parameters.

like_comp(): Likelihood for composition vectors

like_CKMR(): Likelihood for CKMR

Miscellaneous

Other useful functions.

calc_LAK(): Length-at-age key

calc_growth(): Calculate von Bertalanffy length-at-age

CondExpLt() CondExpLe() CondExpGt() CondExpGe() CondExpEq(): If statements compatible with RTMB

conv_Sigma(): Calculate covariance matrix

get_MARSdata(): Retrieve data object used to fit model

get_sdreport(): Calculate standard errors

optimize_RTMB(): Optimize RTMB model

posfun(): Quadratic penalty function

softmax(): Softmax function