_pkgdown.yml

url: https://blue-matter.github.io/MARS/
template:
  bootstrap: 5
  bootswatch: spacelab

navbar:
  components:
    articles:
      text: Topics
      menu:
      - text: Introduction
        href: articles/introduction.html
      - text: Model equations
        href: articles/equations.html

reference:

- title: internal
  contents:
  - Dmodel-class
  - Dstock-class
  - Dfishery-class
  - Dsurvey-class
  - DCKMR-class
  - Dtag-class
  - Dlabel-class
  - plot-MARS-state
  - plot-MARS-data

- title: Data
  desc: S4 objects for data setup.
  contents:
  - MARSdata-class

- title: Model setup
  desc: Prepare the data and parameters, then run the model.
  contents:
  - check_data
  - make_parameters
  - prior
  - fit_MARS
  - MARSassess-class

- title: Model evaluation
  desc: Evaluate model fit and run diagnostics.
  contents:
  - profile
  - report
  - residuals.MARSassess
  - retrospective
  - simulate

- title: Population dynamics
  desc: Functions used in the population model.
  contents:
  - calc_F
  - calc_POP
  - calc_index
  - calc_nextN
  - calc_phi_project
  - calc_phi_simple
  - calc_population
  - calc_recruitment
  - conv_mov
  - conv_selpar
  - calc_eqdist

- title: Likelihood and prior functions
  desc: Calculate the log-likelihood or log-prior density functions from data and estimated parameters.
  contents:
  - like_comp
  - like_CKMR

- title: Miscellaneous
  desc: Other useful functions.
  contents:
  - calc_LAK
  - calc_growth
  - CondExpLt
  - conv_Sigma
  - get_MARSdata
  - get_sdreport
  - optimize_RTMB
  - posfun
  - softmax